Variant report

Variant	rs6956002
Chromosome Location	chr7:150072038-150072039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:150069798-150072038	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:150071081-150072045	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:150069346-150072105	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:150071155-150072110	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr7:150071227-150072125	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr7:150071241-150072073	GM12892	blood:	n/a	n/a
7	POLR2A	chr7:150071218-150072139	K562	blood:	n/a	n/a
8	POLR2A	chr7:150071258-150072062	GM12891	blood:	n/a	n/a
9	POLR2A	chr7:150065010-150072093	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:150071025-150072067	K562	blood:	n/a	n/a
11	POLR2A	chr7:150071162-150072097	A549	lung:	n/a	n/a
12	POLR2A	chr7:150071462-150072068	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr7:150068924-150072074	HL-60	blood:	n/a	n/a
14	POLR2A	chr7:150068187-150072706	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr7:150071065-150072041	K562	blood:	n/a	n/a
16	POLR2A	chr7:150064952-150072087	GM12892	blood:	n/a	n/a
17	POLR2A	chr7:150071489-150072046	GM12891	blood:	n/a	n/a
18	POLR2A	chr7:150064843-150076606	K562	blood:	n/a	n/a
19	POLR2A	chr7:150069673-150072066	GM12892	blood:	n/a	n/a
20	POLR2A	chr7:150071218-150077938	HepG2	liver:	n/a	n/a
21	POLR2A	chr7:150071249-150072044	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:150071154-150072060	GM12891	blood:	n/a	n/a
23	POLR2A	chr7:150064982-150072072	HL-60	blood:	n/a	n/a
24	POLR2A	chr7:150070474-150072073	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:150063876..150080670-chr7:150093696..150109118,65	MCF-7	breast:
2	chr7:149552909..149554975-chr7:150070039..150072542,2	MCF-7	breast:
3	chr7:150035829..150037817-chr7:150071967..150074037,2	MCF-7	breast:
4	chr7:150019286..150021465-chr7:150069323..150073240,4	MCF-7	breast:
5	chr7:150013799..150016585-chr7:150070801..150072302,2	K562	blood:
6	chr7:150026034..150028099-chr7:150070313..150072987,2	K562	blood:
7	chr7:150026422..150030526-chr7:150071487..150075243,4	K562	blood:
8	chr7:150038114..150039918-chr7:150071054..150073165,2	MCF-7	breast:
9	chr7:150020405..150023370-chr7:150070906..150072789,2	K562	blood:
10	chr7:150016043..150018728-chr7:150071723..150073696,2	MCF-7	breast:
11	chr7:150071971..150072481-chr9:4679429..4680093,2	NB4	blood:

No data

Variant related genes	Relation type
ZNF775	TF binding region
ENSG00000240449	TF binding region
ENSG00000106538	Chromatin interaction
ENSG00000273061	Chromatin interaction
ENSG00000106479	Chromatin interaction
ENSG00000106993	Chromatin interaction
ENSG00000261305	Chromatin interaction
ENSG00000127399	Chromatin interaction
ENSG00000188707	Chromatin interaction
ENSG00000106526	Chromatin interaction
ENSG00000196456	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10480297	0.85[ASN][1000 genomes]
rs11762223	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11773825	0.82[ASN][1000 genomes]
rs17173702	0.88[ASN][1000 genomes]
rs17173703	0.88[ASN][1000 genomes]
rs6946097	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6946153	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71537958	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv889453	chr7:150009838-150104410	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv889454	chr7:150009838-150115183	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv889455	chr7:150013393-150104410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv889456	chr7:150013393-150115183	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv889457	chr7:150020295-150104410	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
11	nsv889458	chr7:150020295-150115183	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv521407	chr7:150020295-150118590	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv465211	chr7:150035526-150104410	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
14	nsv608991	chr7:150035526-150104410	Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
15	nsv608992	chr7:150045910-150115183	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
16	esv1819714	chr7:150055837-150154944	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
17	nsv889460	chr7:150060163-150079459	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
18	nsv889461	chr7:150060163-150081485	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
19	nsv889462	chr7:150060163-150108536	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6956002	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs6956002	LRRC61	cis	Muscle Skeletal	GTEx
rs6956002	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs6956002	LRRC61	cis	Nerve Tibial	GTEx
rs6956002	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs6956002	REPIN1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150065400-150073600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr7:150068000-150073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr7:150068000-150073000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:150068000-150073000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:150068200-150073400	Weak transcription	Fetal Kidney	kidney
6	chr7:150068200-150075400	Weak transcription	HMEC	breast
7	chr7:150068400-150074000	Genic enhancers	Fetal Intestine Small	intestine
8	chr7:150068800-150072400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:150068800-150075200	Weak transcription	NH-A	brain
10	chr7:150069000-150075200	Weak transcription	Fetal Brain Male	brain
11	chr7:150069200-150072200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:150069600-150072600	Genic enhancers	Fetal Thymus	thymus
13	chr7:150070000-150075400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:150070000-150075400	Weak transcription	Aorta	Aorta
15	chr7:150070200-150072800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:150070200-150074000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:150070400-150073000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:150070400-150075200	Weak transcription	Psoas Muscle	Psoas
19	chr7:150070400-150075600	Weak transcription	Ovary	ovary
20	chr7:150070600-150075200	Weak transcription	Small Intestine	intestine
21	chr7:150070600-150075600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr7:150070800-150072600	Strong transcription	Brain Anterior Caudate	brain
23	chr7:150070800-150072600	Strong transcription	Fetal Stomach	stomach
24	chr7:150070800-150073200	Weak transcription	Stomach Mucosa	stomach
25	chr7:150070800-150075200	Weak transcription	NHEK	skin
26	chr7:150071000-150072800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr7:150071000-150074600	Weak transcription	Fetal Lung	lung
28	chr7:150071200-150073000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:150071200-150073200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:150071200-150073600	Enhancers	HepG2	liver
31	chr7:150071400-150072200	Genic enhancers	K562	blood
32	chr7:150071400-150072400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:150071400-150072400	Weak transcription	Colonic Mucosa	Colon
34	chr7:150071400-150073800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:150071400-150074800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:150071400-150075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:150071400-150075400	Weak transcription	Right Ventricle	heart
38	chr7:150071600-150073200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:150071600-150075000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr7:150071600-150075200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr7:150071600-150075200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:150071600-150075200	Weak transcription	Colon Smooth Muscle	Colon
43	chr7:150071800-150072400	Weak transcription	Liver	Liver
44	chr7:150071800-150072600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:150071800-150072600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:150071800-150072600	Strong transcription	Fetal Muscle Leg	muscle
47	chr7:150071800-150072800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:150071800-150072800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:150071800-150072800	Weak transcription	HSMMtube	muscle
50	chr7:150071800-150073000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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