Variant report

Variant	rs2071038
Chromosome Location	chr2:98261636-98261637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:98261488-98263007	A549	lung:	n/a	chr2:98262404-98262414
2	SIN3AK20	chr2:98261557-98263138	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:98261353-98263086	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr2:98261600-98262815	NB4	blood:	n/a	chr2:98262404-98262414
5	POLR2A	chr2:98261542-98263124	HL-60	blood:	n/a	n/a
6	JUN	chr2:98261598-98262747	K562	blood:	n/a	n/a
7	POLR2A	chr2:98261628-98263070	PFSK-1	brain:	n/a	n/a
8	RFX5	chr2:98261592-98261784	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:98261549-98262845	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr2:98261582-98262860	GM12891	blood:	n/a	n/a
11	REST	chr2:98261614-98263063	H1-neurons	neurons:	n/a	chr2:98261959-98261968 chr2:98261928-98261942
12	POLR2A	chr2:98261593-98263085	K562	blood:	n/a	n/a
13	POLR2A	chr2:98261634-98262909	GM19099	blood:	n/a	n/a
14	POLR2A	chr2:98261394-98263167	Raji	blood:	n/a	n/a
15	MAX	chr2:98261499-98262743	K562	blood:	n/a	chr2:98262404-98262414
16	POLR2A	chr2:98261359-98263035	K562	blood:	n/a	n/a
17	POLR2A	chr2:98261496-98262938	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr2:98261559-98263254	SK-N-MC	brain:	n/a	n/a
19	SPI1	chr2:98261578-98262060	HL-60	blood:	n/a	chr2:98261864-98261877
20	MAFK	chr2:98261635-98262631	K562	blood:	n/a	chr2:98261904-98261919
21	HEY1	chr2:98261619-98262821	K562	blood:	n/a	n/a
22	POLR2A	chr2:98261386-98262983	K562	blood:	n/a	n/a
23	EP300	chr2:98261609-98262687	GM12878	blood:	n/a	chr2:98262520-98262527 chr2:98262488-98262495
24	POLR2A	chr2:98261543-98262884	K562	blood:	n/a	n/a
25	MAX	chr2:98261333-98262978	K562	blood:	n/a	chr2:98262404-98262414
26	MAX	chr2:98261443-98261879	H1-hESC	embryonic stem cell:	n/a	n/a
27	EP300	chr2:98261570-98262670	K562	blood:	n/a	chr2:98262520-98262527 chr2:98262488-98262495
28	POLR2A	chr2:98261565-98262863	PFSK-1	brain:	n/a	n/a
29	MTA3	chr2:98261525-98262891	GM12878	blood:	n/a	n/a
30	JUND	chr2:98261574-98262662	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:98261334-98262883	K562	blood:	n/a	n/a
32	POLR2A	chr2:98261543-98262960	GM12878	blood:	n/a	n/a
33	CBX3	chr2:98261568-98262795	K562	blood:	n/a	n/a
34	ELF1	chr2:98261627-98262844	K562	blood:	n/a	chr2:98261846-98261857 chr2:98262517-98262528 chr2:98262518-98262527 chr2:98262485-98262496 chr2:98262486-98262495
35	TBL1XR1	chr2:98261634-98262759	K562	blood:	n/a	n/a
36	ZC3H11A	chr2:98261501-98262580	K562	blood:	n/a	n/a
37	POLR2A	chr2:98260388-98263015	K562	blood:	n/a	n/a
38	MAZ	chr2:98261421-98263031	IMR90	lung:	n/a	chr2:98262404-98262414
39	POLR2A	chr2:98261588-98263078	GM12878	blood:	n/a	n/a
40	GABPA	chr2:98261619-98263022	MCF-7	breast:	n/a	chr2:98262386-98262397 chr2:98262383-98262397 chr2:98262338-98262347 chr2:98262386-98262400
41	POLR2A	chr2:98261518-98263107	K562	blood:	n/a	n/a
42	CUX1	chr2:98261584-98262335	K562	blood:	n/a	n/a
43	TBP	chr2:98261551-98263019	K562	blood:	n/a	n/a
44	MYC	chr2:98261386-98262931	K562	blood:	n/a	chr2:98262404-98262414
45	POLR2A	chr2:98261373-98262991	K562	blood:	n/a	n/a
46	POLR2A	chr2:98261612-98263085	K562	blood:	n/a	n/a
47	ZNF263	chr2:98261225-98262772	HEK293-T-REx	kidney:	n/a	chr2:98261967-98261976 chr2:98261861-98261882 chr2:98261875-98261884
48	POLR2A	chr2:98261569-98262793	GM12891	blood:	n/a	n/a
49	WRNIP1	chr2:98261627-98262766	GM12878	blood:	n/a	n/a
50	NRF1	chr2:98261623-98261928	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:98261015..98264268-chr2:98289158..98291782,3	K562	blood:
2	chr2:98260499..98265219-chr2:98284794..98288071,4	MCF-7	breast:
3	chr2:98204043..98208769-chr2:98260858..98263741,4	MCF-7	breast:

Variant related genes	Relation type
COX5B	TF binding region
ENSG00000228486	Chromatin interaction
ENSG00000196912	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs17028771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17695937	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2290123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290126	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2922614	1.00[AMR][1000 genomes]
rs34459720	1.00[ASN][1000 genomes]
rs35321033	1.00[ASN][1000 genomes]
rs35530168	1.00[ASN][1000 genomes]
rs4069515	1.00[AMR][1000 genomes]
rs55757705	1.00[ASN][1000 genomes]
rs55766309	1.00[ASN][1000 genomes]
rs55933640	1.00[ASN][1000 genomes]
rs56035334	1.00[ASN][1000 genomes]
rs56233535	1.00[ASN][1000 genomes]
rs56717024	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58184071	1.00[AMR][1000 genomes]
rs58321192	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58383658	0.86[ASN][1000 genomes]
rs58738348	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59021370	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59060391	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59168350	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59523945	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60226695	0.83[EUR][1000 genomes]
rs60753457	1.00[AMR][1000 genomes]
rs62157581	1.00[ASN][1000 genomes]
rs6542982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716208	1.00[AMR][1000 genomes]
rs6727416	1.00[CEU][hapmap]
rs6753752	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942846	1.00[AMR][1000 genomes]
rs72942852	1.00[AMR][1000 genomes]
rs72942859	1.00[AMR][1000 genomes]
rs72946446	1.00[AMR][1000 genomes]
rs72946451	1.00[AMR][1000 genomes]
rs72947032	1.00[AMR][1000 genomes]
rs72947033	1.00[AMR][1000 genomes]
rs72947062	1.00[AMR][1000 genomes]
rs72949064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949085	1.00[AMR][1000 genomes]
rs72949092	1.00[AMR][1000 genomes]
rs72949095	1.00[AMR][1000 genomes]
rs72951131	0.94[ASN][1000 genomes]
rs7425883	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7563002	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs7608385	0.94[LWK][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv431402	chr2:97669032-98281634	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv535831	chr2:97671335-98270990	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	esv2752937	chr2:97708611-98269110	Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	esv2756939	chr2:97708611-98274527	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv2763630	chr2:97731133-98279050	Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv431413	chr2:97753585-98274527	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv522486	chr2:97768178-98265491	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv869602	chr2:97820572-98263438	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv1005903	chr2:97872625-98264679	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv999118	chr2:97886322-98264679	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv1011958	chr2:97886322-98269110	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv1001249	chr2:97972600-98274527	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv1005846	chr2:97972600-98281634	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
16	nsv1010905	chr2:98013814-98269110	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv1003384	chr2:98013814-98270884	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv1010167	chr2:98013814-98273619	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv999627	chr2:98013814-98274527	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv1009263	chr2:98013814-98281634	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	esv1837228	chr2:98234236-98261636	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
23	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2071038	LOC375249	cis	multi-tissue	Pritchard
rs2071038	COX5B	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98260800-98261800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:98261000-98262000	Enhancers	Spleen	Spleen
3	chr2:98261400-98261800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr2:98261400-98261800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:98261400-98261800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:98261400-98261800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:98261400-98261800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:98261400-98261800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:98261400-98261800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:98261400-98261800	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr2:98261400-98261800	Enhancers	Fetal Thymus	thymus
12	chr2:98261400-98261800	Enhancers	Pancreas	Pancrea
13	chr2:98261400-98261800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:98261400-98261800	Flanking Active TSS	Stomach Mucosa	stomach
15	chr2:98261400-98261800	Flanking Active TSS	GM12878-XiMat	blood
16	chr2:98261400-98261800	Flanking Active TSS	HepG2	liver
17	chr2:98261400-98262000	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr2:98261400-98262000	Enhancers	Fetal Heart	heart
19	chr2:98261400-98262200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr2:98261400-98262200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:98261400-98262200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:98261400-98262200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:98261400-98262200	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr2:98261400-98262200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr2:98261400-98262200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr2:98261400-98262200	Flanking Active TSS	Dnd41	blood
27	chr2:98261400-98262200	Flanking Active TSS	K562	blood
28	chr2:98261400-98262200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr2:98261400-98263200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr2:98261400-98263400	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr2:98261400-98263400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:98261400-98263400	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr2:98261400-98263400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr2:98261400-98263400	Active TSS	Brain Angular Gyrus	brain
35	chr2:98261400-98263400	Active TSS	Fetal Brain Female	brain
36	chr2:98261400-98263400	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr2:98261400-98263600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr2:98261400-98263600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:98261400-98263800	Active TSS	Right Ventricle	heart
40	chr2:98261600-98261800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:98261600-98261800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr2:98261600-98261800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:98261600-98261800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr2:98261600-98261800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:98261600-98261800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:98261600-98261800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:98261600-98261800	Flanking Active TSS	Colonic Mucosa	Colon
48	chr2:98261600-98261800	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr2:98261600-98261800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr2:98261600-98261800	Flanking Active TSS	Fetal Kidney	kidney

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