Variant report

Variant	rs61439415
Chromosome Location	chr2:32502507-32502508
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	POLR2A	chr2:32502015-32503541	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:32502428-32503461	K562	blood:	n/a	n/a
3	STAT5A	chr2:32502390-32503264	K562	blood:	n/a	chr2:32502840-32502854
4	POLR2A	chr2:32502444-32503612	Hela-S3	cervix:	n/a	n/a
5	MAX	chr2:32502059-32503694	HepG2	liver:	n/a	n/a
6	SP1	chr2:32502493-32503402	A549	lung:	n/a	chr2:32502926-32502947
7	TCF12	chr2:32502417-32503520	A549	lung:	n/a	n/a
8	CHD1	chr2:32502463-32503254	GM12878	blood:	n/a	n/a
9	ELF1	chr2:32502486-32503490	HCT-116	colon:	n/a	chr2:32503150-32503159
10	GABPA	chr2:32502505-32503021	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:32502471-32503365	U87	brain:	n/a	n/a
12	POLR2A	chr2:32502078-32503495	HepG2	liver:	n/a	n/a
13	SIN3AK20	chr2:32502502-32503838	MCF-7	breast:	n/a	n/a
14	REST	chr2:32502329-32503807	H1-neurons	neurons:	n/a	n/a
15	NFYB	chr2:32502498-32503093	Hela-S3	cervix:	n/a	chr2:32502925-32502940 chr2:32502898-32502913 chr2:32502925-32502939 chr2:32502925-32502940
16	MYBL2	chr2:32502249-32503491	HepG2	liver:	n/a	n/a
17	TBL1XR1	chr2:32502505-32503198	K562	blood:	n/a	n/a
18	SP1	chr2:32502454-32503373	HCT-116	colon:	n/a	chr2:32502926-32502947
19	POLR2A	chr2:32502402-32503483	GM12878	blood:	n/a	n/a
20	MAFK	chr2:32502477-32503023	K562	blood:	n/a	n/a
21	FOXA1	chr2:32502487-32503168	HepG2	liver:	n/a	n/a
22	MYBL2	chr2:32502060-32503493	HepG2	liver:	n/a	n/a
23	TBL1XR1	chr2:32502368-32503169	K562	blood:	n/a	n/a
24	POLR2A	chr2:32502413-32503703	U87	brain:	n/a	n/a
25	PML	chr2:32502206-32503850	GM12878	blood:	n/a	chr2:32502548-32502556
26	GABPA	chr2:32502454-32503507	MCF-7	breast:	n/a	n/a
27	HCFC1	chr2:32502165-32503757	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr2:32502006-32503602	GM12891	blood:	n/a	n/a
29	POLR2A	chr2:32502364-32503992	GM12878	blood:	n/a	n/a
30	ARID3A	chr2:32502441-32503389	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:32502490-32503388	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr2:32502156-32502526	HCT-116	colon:	n/a	n/a
33	POLR2A	chr2:32502455-32503577	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr2:32502503-32503207	SK-N-SH	brain:	n/a	n/a
35	UBTF	chr2:32502503-32503280	K562	blood:	n/a	n/a
36	ETS1	chr2:32502404-32503312	A549	lung:	n/a	chr2:32502876-32502892 chr2:32502879-32502888 chr2:32502858-32502873 chr2:32502879-32502888
37	CHD2	chr2:32502507-32503485	GM12878	blood:	n/a	n/a
38	SREBP2	chr2:32502179-32504006	GM12878	blood:	n/a	n/a
39	ELK1	chr2:32502475-32503072	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:32502074-32504035	MCF10A-Er-Src	breast:	n/a	n/a
41	GABPA	chr2:32502360-32503367	A549	lung:	n/a	n/a
42	MBD4	chr2:32502503-32503503	HepG2	liver:	n/a	n/a
43	REST	chr2:32502260-32503305	A549	lung:	n/a	n/a
44	ELF1	chr2:32502494-32503294	MCF-7	breast:	n/a	chr2:32503150-32503159
45	GABPA	chr2:32502458-32503244	HL-60	blood:	n/a	n/a
46	GABPA	chr2:32502128-32503466	MCF-7	breast:	n/a	n/a
47	FOXA2	chr2:32501827-32503417	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:32502339-32503787	H1-hESC	embryonic stem cell:	n/a	n/a
49	EP300	chr2:32502226-32503098	K562	blood:	n/a	chr2:32502880-32502887
50	NFIC	chr2:32502393-32503483	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:32389277..32392458-chr2:32500839..32506003,6	K562	blood:
2	chr2:32490466..32494039-chr2:32501355..32504337,3	K562	blood:
3	chr2:32497835..32500252-chr2:32500878..32502905,2	K562	blood:
4	chr2:32490282..32492408-chr2:32501487..32503465,3	MCF-7	breast:

Variant related genes	Relation type
YIPF4	TF binding region
ENSG00000091106	Chromatin interaction
ENSG00000272716	Chromatin interaction
ENSG00000152683	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1046602	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475684	0.82[EUR][1000 genomes]
rs17011943	0.84[EUR][1000 genomes]
rs35368935	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952257	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952258	0.80[AMR][1000 genomes]
rs4952259	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952260	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55788900	0.82[EUR][1000 genomes]
rs57813560	0.82[EUR][1000 genomes]
rs61045200	1.00[ASN][1000 genomes]
rs62134039	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134043	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134044	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134045	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134050	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134052	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134054	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134059	0.84[EUR][1000 genomes]
rs62136263	0.82[EUR][1000 genomes]
rs62136264	0.82[EUR][1000 genomes]
rs62136278	0.82[EUR][1000 genomes]
rs62136279	0.80[EUR][1000 genomes]
rs72798728	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798733	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv1002120	chr2:32470452-32539443	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1004279	chr2:32470452-32543369	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32501400-32502600	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr2:32502000-32502800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr2:32502000-32504000	Active TSS	Psoas Muscle	Psoas
4	chr2:32502200-32502600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:32502200-32502600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr2:32502200-32502600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:32502200-32502600	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr2:32502200-32502600	Flanking Active TSS	Liver	Liver
9	chr2:32502200-32502600	Flanking Active TSS	Brain Angular Gyrus	brain
10	chr2:32502200-32502600	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr2:32502200-32502600	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr2:32502200-32502600	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr2:32502200-32502600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr2:32502200-32502600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:32502200-32502600	Flanking Active TSS	Fetal Kidney	kidney
16	chr2:32502200-32502600	Flanking Active TSS	Rectal Smooth Muscle	rectum
17	chr2:32502200-32502600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr2:32502200-32502600	Flanking Active TSS	A549	lung
19	chr2:32502200-32502600	Flanking Active TSS	GM12878-XiMat	blood
20	chr2:32502200-32502600	Flanking Active TSS	K562	blood
21	chr2:32502200-32502800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr2:32502200-32502800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:32502200-32502800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr2:32502200-32502800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr2:32502200-32502800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr2:32502200-32502800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:32502200-32502800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:32502200-32502800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:32502200-32502800	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr2:32502200-32502800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:32502200-32502800	Flanking Active TSS	Fetal Lung	lung
32	chr2:32502200-32502800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr2:32502200-32502800	Flanking Active TSS	Dnd41	blood
34	chr2:32502200-32502800	Flanking Active TSS	Hela-S3	cervix
35	chr2:32502200-32502800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr2:32502200-32504000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr2:32502200-32504200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:32502200-32504200	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr2:32502200-32504400	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr2:32502200-32504400	Active TSS	Stomach Smooth Muscle	stomach
41	chr2:32502400-32502600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr2:32502400-32502600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:32502400-32502600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:32502400-32502600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:32502400-32502600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:32502400-32502600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:32502400-32502600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:32502400-32502600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:32502400-32502600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:32502400-32502600	Flanking Active TSS	Brain Germinal Matrix	brain

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