Variant report

Variant	rs3816479
Chromosome Location	chr2:33500848-33500849
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	FOXA2	chr2:33500613-33501169	A549	lung:	n/a	n/a
2	USF1	chr2:33500829-33501143	SK-N-SH_RA	brain:	n/a	n/a
3	USF1	chr2:33500799-33501251	K562	blood:	n/a	n/a
4	FOS	chr2:33500800-33501191	HUVEC	blood vessel:	n/a	chr2:33500989-33501000 chr2:33500991-33500999 chr2:33500964-33500975
5	EP300	chr2:33500681-33501221	A549	lung:	n/a	n/a
6	CBX3	chr2:33500725-33501185	K562	blood:	n/a	n/a
7	NR3C1	chr2:33500796-33501115	A549	lung:	n/a	chr2:33500991-33501000
8	MAX	chr2:33500665-33501394	A549	lung:	n/a	chr2:33501253-33501262
9	ATF1	chr2:33500792-33501145	K562	blood:	n/a	n/a
10	MAFF	chr2:33500826-33501118	HepG2	liver:	n/a	n/a
11	STAT3	chr2:33500792-33501366	MCF10A-Er-Src	breast:	n/a	n/a
12	PBX3	chr2:33500701-33501322	SK-N-SH	brain:	n/a	n/a
13	FOSL2	chr2:33500744-33501202	A549	lung:	n/a	chr2:33500991-33500999 chr2:33500963-33500974 chr2:33500988-33500999
14	FOSL2	chr2:33500765-33501256	SK-N-SH	brain:	n/a	chr2:33500991-33500999 chr2:33500963-33500974 chr2:33500988-33500999
15	EP300	chr2:33500673-33501404	SK-N-SH	brain:	n/a	chr2:33501251-33501265
16	TAF1	chr2:33500785-33501121	SK-N-SH	brain:	n/a	n/a
17	SP1	chr2:33500622-33501282	A549	lung:	n/a	n/a
18	JUND	chr2:33500685-33501214	A549	lung:	n/a	chr2:33500991-33500999 chr2:33500989-33501000 chr2:33500964-33500975
19	SP1	chr2:33500592-33501282	A549	lung:	n/a	n/a
20	TCF12	chr2:33500612-33501287	A549	lung:	n/a	n/a
21	RAD21	chr2:33500806-33501202	SK-N-SH_RA	brain:	n/a	n/a
22	FOSL1	chr2:33500687-33501231	HCT-116	colon:	n/a	chr2:33500991-33500999 chr2:33500989-33501000 chr2:33500964-33500975
23	USF1	chr2:33500802-33501231	SK-N-SH	brain:	n/a	n/a
24	STAT3	chr2:33500784-33501254	MCF10A-Er-Src	breast:	n/a	n/a
25	GATA3	chr2:33500660-33501493	SK-N-SH	brain:	n/a	chr2:33500994-33501001
26	SETDB1	chr2:33500771-33501200	U2OS	brain:	n/a	n/a
27	RCOR1	chr2:33500847-33501042	HepG2	liver:	n/a	n/a
28	MYC	chr2:33500819-33501282	MCF10A-Er-Src	breast:	n/a	chr2:33501253-33501262
29	KAP1	chr2:33500843-33501150	U2OS	brain:	n/a	n/a
30	RCOR1	chr2:33500792-33501201	K562	blood:	n/a	n/a
31	JUN	chr2:33500783-33501352	HUVEC	blood vessel:	n/a	chr2:33500991-33500999
32	NR3C1	chr2:33500707-33501166	A549	lung:	n/a	chr2:33500991-33501000
33	STAT3	chr2:33500764-33501225	MCF10A-Er-Src	breast:	n/a	n/a
34	MAFK	chr2:33500834-33501115	K562	blood:	n/a	n/a
35	REST	chr2:33500657-33501215	A549	lung:	n/a	n/a
36	MAX	chr2:33500705-33501268	SK-N-SH	brain:	n/a	chr2:33501253-33501262
37	POLR2A	chr2:33500707-33501246	U87	brain:	n/a	n/a
38	ZBTB33	chr2:33500744-33501107	A549	lung:	n/a	n/a
39	JUND	chr2:33500666-33501380	SK-N-SH	brain:	n/a	chr2:33500991-33500999 chr2:33500989-33501000 chr2:33500964-33500975
40	JUN	chr2:33500831-33501164	K562	blood:	n/a	chr2:33500991-33500999
41	MYBL2	chr2:33500671-33501220	HepG2	liver:	n/a	n/a
42	POLR2A	chr2:33500740-33501267	U87	brain:	n/a	n/a
43	GABPA	chr2:33500673-33501198	A549	lung:	n/a	n/a
44	RAD21	chr2:33500779-33501179	IMR90	lung:	n/a	n/a
45	REST	chr2:33500760-33501115	SK-N-SH	brain:	n/a	n/a
46	NFIC	chr2:33500690-33501419	SK-N-SH	brain:	n/a	n/a
47	FOS	chr2:33500767-33501264	MCF10A-Er-Src	breast:	n/a	chr2:33500989-33501000 chr2:33500991-33500999 chr2:33500964-33500975
48	MAZ	chr2:33500743-33501216	K562	blood:	n/a	n/a
49	NR3C1	chr2:33500698-33501189	A549	lung:	n/a	chr2:33500991-33501000
50	RCOR1	chr2:33500681-33501407	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33169785..33172664-chr2:33500827..33503324,2	K562	blood:

Variant related genes	Relation type
LTBP1	TF binding region
ENSG00000206951	Chromatin interaction
ENSG00000049323	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11883651	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12468099	0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13034772	0.84[ASN][1000 genomes]
rs1453845	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs17581939	0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2123769	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3731575	0.92[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3769531	0.87[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3769535	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3769536	0.93[CHD][hapmap]
rs6756709	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs870858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33472000-33516600	Weak transcription	Psoas Muscle	Psoas
2	chr2:33487000-33509800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:33487800-33502400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:33490600-33515600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:33491800-33502000	Weak transcription	Brain Angular Gyrus	brain
6	chr2:33491800-33504400	Weak transcription	Colonic Mucosa	Colon
7	chr2:33492000-33515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:33492200-33501000	Weak transcription	Placenta	Placenta
9	chr2:33492200-33516600	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:33492200-33516600	Weak transcription	Brain Substantia Nigra	brain
11	chr2:33492400-33501000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:33492400-33501800	Weak transcription	Lung	lung
13	chr2:33492400-33502000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:33492400-33502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:33492400-33502000	Weak transcription	Spleen	Spleen
16	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
17	chr2:33492600-33502000	Weak transcription	Ovary	ovary
18	chr2:33492600-33508400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:33493400-33502000	Weak transcription	Fetal Brain Male	brain
20	chr2:33493600-33515200	Weak transcription	Fetal Lung	lung
21	chr2:33493800-33503400	Weak transcription	Fetal Brain Female	brain
22	chr2:33493800-33515400	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:33494000-33502000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:33494200-33506200	Weak transcription	Fetal Heart	heart
25	chr2:33494200-33516000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:33494200-33516200	Weak transcription	Fetal Kidney	kidney
27	chr2:33494600-33515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:33496200-33501000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:33497800-33503400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:33499200-33501200	Strong transcription	NHLF	lung
31	chr2:33499200-33508000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:33499400-33502400	Strong transcription	Liver	Liver
33	chr2:33499600-33501400	Strong transcription	Left Ventricle	heart
34	chr2:33499600-33502200	Strong transcription	Aorta	Aorta
35	chr2:33499800-33501400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:33499800-33501600	Genic enhancers	NH-A	brain
37	chr2:33499800-33502400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:33500000-33501000	Weak transcription	Right Ventricle	heart
39	chr2:33500000-33502200	Strong transcription	Fetal Stomach	stomach
40	chr2:33500000-33502400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:33500200-33501000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:33500200-33501600	Enhancers	HUVEC	blood vessel
43	chr2:33500200-33504800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:33500400-33502400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:33500400-33502600	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr2:33500800-33501000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:33500800-33501000	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr2:33500800-33501000	Enhancers	Gastric	stomach
49	chr2:33500800-33501000	Enhancers	Pancreas	Pancrea
50	chr2:33500800-33501000	Enhancers	HepG2	liver

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