Variant report

Variant	rs6437585
Chromosome Location	chr3:105086085-105086086
allele	C/T
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	chr3:105085026-105088883	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:105085188-105086292	Hela-S3	cervix:	n/a	n/a
3	ELF1	chr3:105085007-105086714	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr3:105084834-105086152	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:105086020-105086170	GM12875	blood:	n/a	n/a
6	MAX	chr3:105085177-105086904	Hela-S3	cervix:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
7	BHLHE40	chr3:105085275-105086170	GM12878	blood:	n/a	chr3:105085461-105085477
8	POLR2A	chr3:105085003-105086355	HEK293	kidney:	n/a	n/a
9	CTCF	chr3:105086060-105086210	SK-N-SH_RA	brain:	n/a	n/a
10	CTCF	chr3:105086003-105086214	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:105084812-105086180	HCT-116	colon:	n/a	n/a
12	MAX	chr3:105086021-105086648	H1-hESC	embryonic stem cell:	n/a	chr3:105086357-105086366
13	SIN3AK20	chr3:105084561-105086326	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr3:105086040-105086190	GM12871	blood:	n/a	n/a
15	POLR2A	chr3:105084872-105086371	Gliobla	brain:	n/a	n/a
16	POLR2A	chr3:105085354-105088882	NB4	blood:	n/a	n/a
17	CTCF	chr3:105085980-105086130	GM12872	blood:	n/a	n/a
18	POLR2A	chr3:105085127-105088862	GM18526	blood:	n/a	n/a
19	POLR2A	chr3:105085112-105088857	Raji	blood:	n/a	n/a
20	POLR2A	chr3:105085099-105088820	GM12892	blood:	n/a	n/a
21	CHD2	chr3:105084939-105086257	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:105084905-105086791	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:105085346-105087180	HL-60	blood:	n/a	n/a
24	BACH1	chr3:105084763-105086335	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr3:105086040-105086190	HRPEpiC	eye:	n/a	n/a
26	RAD21	chr3:105084450-105086202	A549	lung:	n/a	chr3:105085505-105085515
27	EP300	chr3:105085982-105086188	GM12878	blood:	n/a	n/a
28	RCOR1	chr3:105086081-105086833	HepG2	liver:	n/a	n/a
29	MAX	chr3:105085197-105088945	Hela-S3	cervix:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
30	HMGN3	chr3:105086021-105086195	K562	blood:	n/a	n/a
31	MAZ	chr3:105085137-105087117	Hela-S3	cervix:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
32	MYC	chr3:105085993-105086181	MCF-7	breast:	n/a	n/a
33	CREB1	chr3:105085978-105088362	GM12878	blood:	n/a	chr3:105086677-105086690
34	POLR2A	chr3:105085126-105088818	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:105085190-105086468	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr3:105084469-105089450	MCF10A-Er-Src	breast:	n/a	n/a
37	CTCF	chr3:105086000-105086150	AG10803	skin:	n/a	n/a
38	CTCF	chr3:105086069-105086091	ProgFib	skin:	n/a	n/a
39	POLR2A	chr3:105085339-105087101	HepG2	liver:	n/a	n/a
40	CTCF	chr3:105086003-105086217	MCF-7	breast:	n/a	n/a
41	CTCF	chr3:105086078-105086155	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr3:105085196-105086380	H1-neurons	neurons:	n/a	n/a
43	SMARCC1	chr3:105084954-105087287	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr3:105085241-105086118	Hela-S3	cervix:	n/a	n/a
45	MAX	chr3:105084399-105089068	A549	lung:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
46	CTCF	chr3:105085980-105086130	AoAF	blood vessel:	n/a	n/a
47	TAF1	chr3:105084920-105086133	ECC-1	luminal epithelium:	n/a	n/a
48	HA-E2F1	chr3:105084461-105086434	MCF-7	breast:	n/a	n/a
49	POLR2A	chr3:105084982-105088897	Hela-S3	cervix:	n/a	n/a
50	YY1	chr3:105085903-105086180	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:676922..677548-chr3:105085579..105086126,2	Hela-S3	cervix:

Variant related genes	Relation type
ALCAM	TF binding region
ENSG00000151353	Chromatin interaction
ENSG00000233296	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13317567	1.00[MEX][hapmap]
rs16851209	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2033803	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs28444183	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3772558	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs59857604	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6437586	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618632	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7633625	0.89[ASN][1000 genomes]
rs7640337	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650270	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651616	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7651901	0.83[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9815659	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846962	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9848760	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9875972	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9879039	0.89[ASN][1000 genomes]
rs9879710	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105083600-105086400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:105083800-105087800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:105083800-105088800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:105083800-105088800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:105084000-105086200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:105084000-105087600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:105084000-105088800	Active TSS	Brain Substantia Nigra	brain
8	chr3:105084000-105089000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:105084000-105089000	Active TSS	A549	lung
10	chr3:105084000-105089600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:105084200-105087800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:105084200-105088400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:105084200-105089000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:105084200-105089000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:105084200-105089000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:105084200-105089200	Active TSS	NHDF-Ad	bronchial
17	chr3:105084200-105089600	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:105084200-105089600	Active TSS	NHLF	lung
19	chr3:105084200-105090400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:105084400-105086200	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr3:105084400-105086200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:105084400-105086200	Active TSS	Colon Smooth Muscle	Colon
23	chr3:105084400-105086400	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:105084400-105086400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:105084400-105086600	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr3:105084400-105087200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:105084400-105087800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:105084400-105088800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:105084400-105088800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:105084400-105088800	Active TSS	Brain Cingulate Gyrus	brain
31	chr3:105084400-105088800	Active TSS	Gastric	stomach
32	chr3:105084400-105089000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:105084400-105089000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:105084400-105089000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr3:105084400-105089000	Active TSS	Aorta	Aorta
36	chr3:105084400-105089000	Active TSS	Brain Angular Gyrus	brain
37	chr3:105084400-105089000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:105084400-105089000	Active TSS	Ovary	ovary
39	chr3:105084400-105089400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:105084400-105089400	Active TSS	GM12878-XiMat	blood
41	chr3:105084400-105089600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:105084600-105086400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:105084600-105087000	Flanking Bivalent TSS/Enh	Placenta	Placenta
44	chr3:105084600-105087600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
45	chr3:105084600-105088600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr3:105084600-105088600	Active TSS	Small Intestine	intestine
47	chr3:105084600-105088800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr3:105084600-105088800	Active TSS	Esophagus	oesophagus
49	chr3:105084600-105088800	Active TSS	Fetal Heart	heart
50	chr3:105084600-105089000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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