Variant report

Variant	rs6952735
Chromosome Location	chr7:99963573-99963574
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:60)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:60 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99962856-99963615	HCT-116	colon:	n/a	n/a
2	POLR2A	chr7:99961591-99967321	K562	blood:	n/a	n/a
3	POLR2A	chr7:99962778-99963643	SK-N-MC	brain:	n/a	n/a
4	NFATC1	chr7:99962919-99963672	GM12878	blood:	n/a	n/a
5	MAX	chr7:99963011-99963673	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:99961696-99963611	SK-N-SH	brain:	n/a	n/a
7	SP1	chr7:99963286-99963579	GM12878	blood:	n/a	n/a
8	POLR2A	chr7:99961803-99969906	MCF-7	breast:	n/a	n/a
9	POLR2A	chr7:99962791-99965302	HepG2	liver:	n/a	n/a
10	BCL3	chr7:99962808-99963664	A549	lung:	n/a	n/a
11	RUNX3	chr7:99962879-99965138	GM12878	blood:	n/a	n/a
12	POLR2A	chr7:99962922-99965562	GM12892	blood:	n/a	n/a
13	MTA3	chr7:99962771-99965650	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:99961083-99967399	PFSK-1	brain:	n/a	n/a
15	IRF4	chr7:99963304-99963706	GM12878	blood:	n/a	n/a
16	ZNF384	chr7:99963183-99964014	GM12878	blood:	n/a	n/a
17	ATF2	chr7:99962935-99963637	GM12878	blood:	n/a	n/a
18	EP300	chr7:99963026-99964046	GM12878	blood:	n/a	n/a
19	CREB1	chr7:99963133-99963640	GM12878	blood:	n/a	n/a
20	POLR2A	chr7:99962901-99963683	GM12891	blood:	n/a	n/a
21	NFATC1	chr7:99962893-99967425	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:99959279-99970406	K562	blood:	n/a	n/a
23	POLR2A	chr7:99961744-99967551	A549	lung:	n/a	n/a
24	POLR2A	chr7:99962720-99965252	GM12891	blood:	n/a	n/a
25	POLR2A	chr7:99961321-99968296	K562	blood:	n/a	n/a
26	POLR2A	chr7:99962759-99963594	GM12891	blood:	n/a	n/a
27	RUNX3	chr7:99962940-99965265	GM12878	blood:	n/a	n/a
28	CREB1	chr7:99963026-99963662	GM12878	blood:	n/a	n/a
29	POLR2A	chr7:99963512-99963682	GM12878	blood:	n/a	n/a
30	POLR2A	chr7:99962941-99965511	GM12891	blood:	n/a	n/a
31	TBP	chr7:99962961-99963687	GM12878	blood:	n/a	n/a
32	POLR2A	chr7:99962792-99963670	GM12892	blood:	n/a	n/a
33	NFIC	chr7:99962759-99964963	GM12878	blood:	n/a	n/a
34	STAT5A	chr7:99963025-99963659	GM12878	blood:	n/a	n/a
35	IKZF1	chr7:99962900-99964052	GM12878	blood:	n/a	n/a
36	POLR2A	chr7:99962814-99965050	GM12878	blood:	n/a	n/a
37	ATF2	chr7:99962883-99965037	GM12878	blood:	n/a	n/a
38	TBL1XR1	chr7:99963396-99963599	GM12878	blood:	n/a	n/a
39	PML	chr7:99962797-99964821	K562	blood:	n/a	chr7:99964036-99964044
40	EBF1	chr7:99963267-99963615	GM12878	blood:	n/a	n/a
41	POLR2A	chr7:99961228-99967403	PANC-1	pancreas:	n/a	n/a
42	CUX1	chr7:99963456-99963672	GM12878	blood:	n/a	n/a
43	POLR2A	chr7:99961021-99967328	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr7:99963276-99963608	GM12891	blood:	n/a	n/a
45	POLR2A	chr7:99962774-99967568	K562	blood:	n/a	n/a
46	POLR2A	chr7:99962860-99965229	GM12892	blood:	n/a	n/a
47	FOXM1	chr7:99963155-99963650	GM12878	blood:	n/a	n/a
48	POLR2A	chr7:99961913-99969801	HepG2	liver:	n/a	n/a
49	EP300	chr7:99962929-99965027	GM12878	blood:	n/a	n/a
50	EBF1	chr7:99963332-99963654	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99962016..99964222-chr7:99964499..99967537,3	MCF-7	breast:
2	chr7:99955250..99958076-chr7:99963058..99965429,2	K562	blood:
3	chr7:99962514..99964875-chr7:99978012..99980552,2	K562	blood:
4	chr7:99943654..99945784-chr7:99961276..99963907,2	K562	blood:
5	chr7:99961248..99963871-chr7:99971979..99975112,4	K562	blood:
6	chr7:99953591..99956597-chr7:99962899..99966077,3	MCF-7	breast:
7	chr7:99962424..99964406-chr7:100286120..100288953,2	MCF-7	breast:
8	chr7:99962458..99965072-chr7:100011699..100014175,2	K562	blood:

No data

Variant related genes	Relation type
PILRA	TF binding region
ENSG00000121716	Chromatin interaction
ENSG00000085514	Chromatin interaction
ENSG00000146830	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10246363	0.86[YRI][hapmap]
rs6958977	1.00[ASW][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs6968343	1.00[ASW][hapmap];0.95[LWK][hapmap];0.86[YRI][hapmap]
rs6970350	0.89[ASW][hapmap]

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	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv831071	chr7:99918025-100113413	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	287 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6952735	PVRIG	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99934000-99977600	Weak transcription	Fetal Brain Male	brain
2	chr7:99934800-99963800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:99937600-99967800	Strong transcription	Fetal Stomach	stomach
4	chr7:99938600-99967400	Strong transcription	Fetal Brain Female	brain
5	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
6	chr7:99942800-99963600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:99942800-99966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:99942800-99966400	Strong transcription	A549	lung
9	chr7:99942800-99967000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:99942800-99967400	Strong transcription	Fetal Intestine Small	intestine
11	chr7:99943200-99965400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:99943400-99966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:99943400-99967200	Strong transcription	Fetal Intestine Large	intestine
14	chr7:99943800-99963800	Strong transcription	Placenta	Placenta
15	chr7:99944000-99967000	Strong transcription	Brain Anterior Caudate	brain
16	chr7:99944200-99967400	Strong transcription	Brain Germinal Matrix	brain
17	chr7:99945400-99969400	Weak transcription	Fetal Heart	heart
18	chr7:99945600-99966000	Strong transcription	Fetal Muscle Leg	muscle
19	chr7:99946000-99966800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr7:99946400-99967400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:99951600-99964000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:99953000-99963600	Strong transcription	Fetal Thymus	thymus
23	chr7:99957000-99966400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:99957200-99967000	Weak transcription	Stomach Mucosa	stomach
25	chr7:99957800-99965600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:99958200-99963800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr7:99958200-99964000	Weak transcription	NHDF-Ad	bronchial
28	chr7:99959400-99964000	Weak transcription	Colonic Mucosa	Colon
29	chr7:99959600-99964000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:99959600-99964000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr7:99959600-99970200	Weak transcription	HSMM	muscle
32	chr7:99959800-99964000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:99959800-99964000	Weak transcription	Esophagus	oesophagus
34	chr7:99959800-99966800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:99960000-99964600	Weak transcription	Right Ventricle	heart
36	chr7:99960000-99967400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr7:99960200-99963600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:99960200-99964000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr7:99960200-99964000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:99960200-99964600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:99960200-99965400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:99960200-99966400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:99960200-99968400	Weak transcription	Gastric	stomach
44	chr7:99960200-99969000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:99960200-99975400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr7:99960400-99964800	Weak transcription	NHLF	lung
47	chr7:99960400-99984800	Weak transcription	Pancreas	Pancrea
48	chr7:99960600-99964000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:99960600-99964600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:99960600-99967800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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