Variant report

Variant	rs35314132
Chromosome Location	chr7:39772916-39772917
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	GATA3	chr7:39772772-39774169	SK-N-SH	brain:	n/a	n/a
2	SP4	chr7:39772850-39773269	H1-hESC	embryonic stem cell:	n/a	n/a
3	BRCA1	chr7:39772781-39773137	HepG2	liver:	n/a	n/a
4	EGR1	chr7:39772838-39773355	H1-hESC	embryonic stem cell:	n/a	chr7:39773096-39773106 chr7:39773080-39773090 chr7:39773080-39773089 chr7:39773080-39773091 chr7:39773080-39773090 chr7:39773080-39773091 chr7:39773076-39773090
5	POLR2A	chr7:39772903-39773375	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr7:39772663-39773471	GM18951	blood:	n/a	n/a
7	TCF7L2	chr7:39772790-39773343	PANC-1	pancreas:	n/a	n/a
8	SMARCC1	chr7:39772407-39774122	Hela-S3	cervix:	n/a	n/a
9	PBX3	chr7:39772787-39774168	SK-N-SH	brain:	n/a	n/a
10	PML	chr7:39772824-39773432	GM12878	blood:	n/a	n/a
11	TAF1	chr7:39772356-39773446	H1-neurons	neurons:	n/a	n/a
12	EGR1	chr7:39772772-39773380	ECC-1	luminal epithelium:	n/a	chr7:39773096-39773106 chr7:39773080-39773090 chr7:39773080-39773089 chr7:39773080-39773091 chr7:39773080-39773090 chr7:39773080-39773091 chr7:39773076-39773090
13	MAX	chr7:39772553-39773801	A549	lung:	n/a	chr7:39772766-39772781 chr7:39772900-39772910
14	EP300	chr7:39772849-39773297	GM12878	blood:	n/a	n/a
15	UBTF	chr7:39772899-39773350	K562	blood:	n/a	n/a
16	POLR2A	chr7:39772368-39773936	H1-neurons	neurons:	n/a	n/a
17	EGR1	chr7:39772779-39773475	MCF-7	breast:	n/a	chr7:39773096-39773106 chr7:39773080-39773090 chr7:39773080-39773089 chr7:39773080-39773091 chr7:39773080-39773090 chr7:39773080-39773091 chr7:39773076-39773090
18	E2F6	chr7:39772340-39773413	K562	blood:	n/a	chr7:39772967-39772976 chr7:39772969-39772978 chr7:39772494-39772506
19	GABPA	chr7:39772294-39773877	MCF-7	breast:	n/a	n/a
20	MAX	chr7:39772636-39773755	H1-hESC	embryonic stem cell:	n/a	chr7:39772766-39772781 chr7:39772900-39772910
21	PAX5	chr7:39772905-39773248	GM12878	blood:	n/a	n/a
22	USF2	chr7:39772665-39773844	Hela-S3	cervix:	n/a	chr7:39773570-39773581 chr7:39772766-39772779
23	ZNF143	chr7:39772700-39773240	K562	blood:	n/a	n/a
24	BCL3	chr7:39772834-39773402	A549	lung:	n/a	chr7:39773161-39773170
25	ZNF143	chr7:39772612-39773408	GM12878	blood:	n/a	n/a
26	POLR2A	chr7:39772822-39773389	HUVEC	blood vessel:	n/a	n/a
27	RELA	chr7:39772659-39774351	GM18505	blood:	n/a	n/a
28	NFATC1	chr7:39772735-39773377	GM12878	blood:	n/a	n/a
29	MTA3	chr7:39772306-39774112	GM12878	blood:	n/a	n/a
30	POU2F2	chr7:39772652-39773464	GM12878	blood:	n/a	n/a
31	RAD21	chr7:39772593-39774135	IMR90	lung:	n/a	chr7:39773937-39773949 chr7:39773937-39773947
32	USF1	chr7:39772538-39773145	SK-N-SH_RA	brain:	n/a	chr7:39772766-39772779
33	SPI1	chr7:39772368-39773487	HL-60	blood:	n/a	chr7:39772542-39772555 chr7:39772682-39772695 chr7:39772684-39772693 chr7:39772541-39772554 chr7:39772777-39772790
34	TAF1	chr7:39772656-39773278	H1-neurons	neurons:	n/a	n/a
35	SP1	chr7:39772763-39773428	GM12878	blood:	n/a	chr7:39772777-39772786 chr7:39772776-39772788 chr7:39772773-39772787
36	RFX5	chr7:39771932-39773841	H1-hESC	embryonic stem cell:	n/a	chr7:39773044-39773059
37	CTCF	chr7:39772790-39773305	GM12878	blood:	n/a	n/a
38	POLR2A	chr7:39772616-39772979	H1-hESC	embryonic stem cell:	n/a	n/a
39	ELK1	chr7:39772768-39773835	Hela-S3	cervix:	n/a	chr7:39773161-39773170 chr7:39773161-39773170
40	CEBPB	chr7:39772610-39773878	H1-hESC	embryonic stem cell:	n/a	n/a
41	USF2	chr7:39772326-39773280	GM12878	blood:	n/a	chr7:39772766-39772779
42	MAX	chr7:39772747-39773941	Hela-S3	cervix:	n/a	chr7:39772766-39772781 chr7:39772900-39772910
43	IRF1	chr7:39772811-39773180	K562	blood:	n/a	n/a
44	ZNF143	chr7:39772814-39773241	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr7:39772594-39774132	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr7:39772590-39774218	GM12892	blood:	n/a	n/a
47	PAX5	chr7:39772778-39773348	GM12878	blood:	n/a	n/a
48	GABPA	chr7:39772914-39773375	K562	blood:	n/a	n/a
49	CREB1	chr7:39772665-39773358	A549	lung:	n/a	chr7:39772966-39772979
50	CHD2	chr7:39772602-39773942	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39660619..39666370-chr7:39771379..39777121,13	MCF-7	breast:
2	chr7:39605618..39607861-chr7:39772706..39774759,2	K562	blood:
3	chr7:39661063..39664836-chr7:39769831..39775766,6	MCF-7	breast:

Variant related genes	Relation type
LINC00265	TF binding region
ENSG00000241127	Chromatin interaction
ENSG00000006451	Chromatin interaction
ENSG00000227172	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10253933	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10267545	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10486805	0.96[ASN][1000 genomes]
rs11765970	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11773617	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12668144	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12701754	0.89[EUR][1000 genomes]
rs12701756	0.96[ASN][1000 genomes]
rs12701757	0.96[ASN][1000 genomes]
rs12701759	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13244194	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34910913	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35774126	0.90[EUR][1000 genomes]
rs3779200	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62453003	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6977082	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7778955	0.96[ASN][1000 genomes]
rs7779169	0.96[ASN][1000 genomes]
rs7782931	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7797693	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 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	chr7:39772200-39773000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:39772200-39773000	Flanking Active TSS	Fetal Muscle Trunk	muscle
3	chr7:39772200-39773000	Flanking Active TSS	Dnd41	blood
4	chr7:39772200-39773200	Bivalent/Poised TSS	HepG2	liver
5	chr7:39772200-39773400	Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr7:39772200-39773400	Active TSS	Brain Anterior Caudate	brain
7	chr7:39772200-39773400	Active TSS	Brain Hippocampus Middle	brain
8	chr7:39772200-39773400	Active TSS	Placenta Amnion	Placenta Amnion
9	chr7:39772200-39773600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:39772200-39773800	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr7:39772200-39773800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:39772200-39774000	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr7:39772200-39774200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr7:39772200-39774200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr7:39772400-39773000	Flanking Active TSS	GM12878-XiMat	blood
16	chr7:39772400-39773000	Flanking Active TSS	K562	blood
17	chr7:39772400-39773200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:39772400-39773400	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr7:39772400-39773400	Active TSS	Colon Smooth Muscle	Colon
20	chr7:39772400-39773400	Active TSS	Fetal Brain Female	brain
21	chr7:39772400-39773400	Active TSS	A549	lung
22	chr7:39772400-39773600	Active TSS	Brain Angular Gyrus	brain
23	chr7:39772400-39773600	Active TSS	Brain Cingulate Gyrus	brain
24	chr7:39772400-39773600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:39772400-39773600	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr7:39772400-39773600	Active TSS	Psoas Muscle	Psoas
27	chr7:39772400-39773600	Active TSS	Rectal Smooth Muscle	rectum
28	chr7:39772400-39773600	Active TSS	HSMM	muscle
29	chr7:39772400-39773800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:39772400-39774000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr7:39772400-39774000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:39772400-39774000	Flanking Active TSS	Liver	Liver
33	chr7:39772400-39774000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr7:39772400-39774200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:39772400-39774200	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr7:39772400-39774200	Flanking Active TSS	Placenta	Placenta
37	chr7:39772400-39774200	Flanking Active TSS	Fetal Thymus	thymus
38	chr7:39772400-39774200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr7:39772400-39774200	Flanking Active TSS	HUVEC	blood vessel
40	chr7:39772400-39774400	Flanking Active TSS	HMEC	breast
41	chr7:39772600-39773000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:39772600-39773200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:39772600-39773200	Active TSS	Muscle Satellite Cultured Cells	--
44	chr7:39772600-39773200	Transcr. at gene 5' and 3'	Right Atrium	heart
45	chr7:39772600-39773200	Active TSS	NHLF	lung
46	chr7:39772600-39773200	Active TSS	Osteobl	bone
47	chr7:39772600-39773400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr7:39772600-39773400	Active TSS	Brain Substantia Nigra	brain
49	chr7:39772600-39773600	Active TSS	H9 Cell Line	embryonic stem cell
50	chr7:39772600-39773600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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