Variant report

Variant	rs4264585
Chromosome Location	chr2:191334031-191334032
allele	C/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	chr2:191333950-191334985	HUVEC	blood vessel:	n/a	n/a
2	EP300	chr2:191333368-191335652	SK-N-SH	brain:	n/a	n/a
3	IRF1	chr2:191333966-191334264	K562	blood:	n/a	chr2:191334196-191334203
4	MAFK	chr2:191333973-191334290	K562	blood:	n/a	n/a
5	STAT3	chr2:191333937-191334284	MCF10A-Er-Src	breast:	n/a	chr2:191334054-191334066
6	KAP1	chr2:191333573-191334289	U2OS	brain:	n/a	n/a
7	REST	chr2:191333940-191334243	K562	blood:	n/a	n/a
8	FOXP2	chr2:191333879-191334317	SK-N-MC	brain:	n/a	n/a
9	KAP1	chr2:191333489-191334329	HEK293	kidney:	n/a	n/a
10	TCF12	chr2:191333384-191334442	SK-N-SH	brain:	n/a	chr2:191334032-191334041 chr2:191333849-191333858
11	STAT3	chr2:191334011-191334211	MCF10A-Er-Src	breast:	n/a	chr2:191334054-191334066
12	GATA3	chr2:191333715-191334409	MCF-7	breast:	n/a	n/a
13	POLR2A	chr2:191333839-191334439	SK-N-MC	brain:	n/a	n/a
14	SP1	chr2:191333744-191334377	A549	lung:	n/a	chr2:191334059-191334072
15	STAT3	chr2:191333993-191334193	MCF10A-Er-Src	breast:	n/a	chr2:191334054-191334066
16	GATA3	chr2:191333609-191334446	SK-N-SH	brain:	n/a	n/a
17	GATA1	chr2:191333927-191334571	PBDE	blood:	n/a	n/a
18	RCOR1	chr2:191333927-191334329	K562	blood:	n/a	n/a
19	NR3C1	chr2:191333910-191334204	A549	lung:	n/a	n/a
20	YY1	chr2:191333978-191334435	SK-N-SH_RA	brain:	n/a	n/a
21	ARID3A	chr2:191333834-191334379	K562	blood:	n/a	n/a
22	RAD21	chr2:191333902-191334381	SK-N-SH_RA	brain:	n/a	n/a
23	MYC	chr2:191333868-191334272	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr2:191333939-191334299	MCF10A-Er-Src	breast:	n/a	n/a
25	TEAD4	chr2:191333902-191334310	K562	blood:	n/a	n/a
26	MEF2A	chr2:191333876-191334472	SK-N-SH	brain:	n/a	chr2:191334166-191334177
27	MAX	chr2:191333812-191334299	SK-N-SH	brain:	n/a	n/a
28	EP300	chr2:191333892-191334306	K562	blood:	n/a	n/a
29	HMGN3	chr2:191333982-191334176	K562	blood:	n/a	n/a
30	TCF12	chr2:191333596-191334215	ECC-1	luminal epithelium:	n/a	chr2:191334032-191334041 chr2:191333849-191333858
31	GATA3	chr2:191334019-191334301	T-47D	breast:	n/a	n/a
32	GATA3	chr2:191333959-191334438	SH-SY5Y	brain:	n/a	n/a
33	ZNF217	chr2:191333847-191334293	MCF-7	breast:	n/a	n/a
34	FOXA1	chr2:191333918-191334162	ECC-1	luminal epithelium:	n/a	n/a
35	RAD21	chr2:191333958-191334329	SK-N-SH_RA	brain:	n/a	n/a
36	FOSL2	chr2:191333794-191334331	A549	lung:	n/a	n/a
37	PBX3	chr2:191333811-191334414	SK-N-SH	brain:	n/a	n/a
38	FOS	chr2:191333897-191334307	MCF10A-Er-Src	breast:	n/a	n/a
39	REST	chr2:191333982-191334247	SK-N-SH	brain:	n/a	n/a
40	JUND	chr2:191333736-191334453	SK-N-SH	brain:	n/a	n/a
41	NFIC	chr2:191333584-191334399	SK-N-SH	brain:	n/a	n/a
42	EP300	chr2:191333423-191334465	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr2:191334018-191334868	MCF10A-Er-Src	breast:	n/a	n/a
44	NFIC	chr2:191333380-191334410	ECC-1	luminal epithelium:	n/a	n/a
45	STAT3	chr2:191334019-191334221	MCF10A-Er-Src	breast:	n/a	chr2:191334054-191334066
46	EP300	chr2:191333881-191334389	SK-N-SH_RA	brain:	n/a	n/a
47	POLR2A	chr2:191334019-191334253	K562	blood:	n/a	n/a
48	EP300	chr2:191333934-191334373	SK-N-SH_RA	brain:	n/a	n/a
49	CEBPB	chr2:191333833-191334274	Hela-S3	cervix:	n/a	n/a
50	FOXA2	chr2:191333742-191334385	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:191318515..191323057-chr2:191332501..191335066,4	MCF-7	breast:
2	chr2:191272262..191274939-chr2:191333629..191335814,2	MCF-7	breast:
3	chr2:191271631..191274450-chr2:191332507..191334267,2	MCF-7	breast:
4	chr2:191332610..191334392-chr2:191512174..191513999,2	K562	blood:

Variant related genes	Relation type
MFSD6	TF binding region
ENSG00000272979	Chromatin interaction
ENSG00000151690	Chromatin interaction
ENSG00000138386	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10193212	0.83[YRI][hapmap]
rs11897266	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12464923	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12472240	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12473460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12613365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12613807	0.83[YRI][hapmap]
rs12615925	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12619125	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12619560	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621493	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12622496	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12693576	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987797	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13013848	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13019278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13028201	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13029743	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13391723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34274882	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34417560	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34825614	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36055519	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3811609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073873	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129081	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4324342	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4586658	0.89[LWK][hapmap]
rs4853508	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4853709	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4853718	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4853720	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55754136	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55987230	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6434400	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6707773	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6707846	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6711006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72911109	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560318	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584794	0.85[LWK][hapmap]
rs7601745	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608180	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4264585	HIBCH	cis	cerebellum	SCAN
rs4264585	HIBCH	cis	parietal	SCAN
rs4264585	FLJ20160	cis	multi-tissue	Pritchard
rs4264585	INPP1	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
2	chr2:191322000-191335800	Weak transcription	Esophagus	oesophagus
3	chr2:191322600-191335600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:191323000-191334600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:191323200-191335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:191325600-191335800	Weak transcription	Lung	lung
7	chr2:191325600-191346200	Weak transcription	Right Ventricle	heart
8	chr2:191327600-191353000	Weak transcription	Primary B cells from cord blood	blood
9	chr2:191328800-191334400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:191328800-191334600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:191329600-191334600	Weak transcription	Thymus	Thymus
12	chr2:191330000-191334800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:191330200-191334800	Enhancers	K562	blood
14	chr2:191330600-191335200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:191330800-191334800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:191330800-191335400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:191330800-191335400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:191331000-191334400	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr2:191331000-191334800	Enhancers	NHDF-Ad	bronchial
20	chr2:191331000-191335000	Enhancers	Brain Substantia Nigra	brain
21	chr2:191331000-191335200	Enhancers	Brain Cingulate Gyrus	brain
22	chr2:191331000-191335400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:191331000-191335400	Enhancers	Hela-S3	cervix
24	chr2:191331000-191335400	Enhancers	Osteobl	bone
25	chr2:191331200-191335400	Enhancers	NHLF	lung
26	chr2:191331200-191335600	Enhancers	Fetal Lung	lung
27	chr2:191331400-191334200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr2:191331400-191334400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr2:191331400-191334400	Enhancers	Fetal Brain Male	brain
30	chr2:191331400-191334800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:191331400-191334800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:191331400-191335000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:191331400-191335000	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:191331400-191335200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:191331400-191335200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:191331400-191335400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:191331400-191335400	Enhancers	Brain Angular Gyrus	brain
38	chr2:191331400-191335400	Enhancers	Fetal Heart	heart
39	chr2:191331400-191335400	Enhancers	Fetal Muscle Leg	muscle
40	chr2:191331400-191335400	Enhancers	Fetal Stomach	stomach
41	chr2:191331400-191335600	Enhancers	Colon Smooth Muscle	Colon
42	chr2:191331600-191334200	Enhancers	Fetal Brain Female	brain
43	chr2:191331600-191334400	Enhancers	Adipose Nuclei	Adipose
44	chr2:191331600-191334600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:191331600-191334800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:191331600-191334800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:191331600-191334800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:191331600-191335000	Genic enhancers	Primary T cells from cord blood	blood
49	chr2:191331600-191335400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr2:191331600-191335400	Enhancers	Stomach Mucosa	stomach

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