Variant report

Variant	rs6967282
Chromosome Location	chr7:150907194-150907195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:150906939-150907290	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:150903944-150907362	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr7:150906323-150907343	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr7:150907018-150907372	GM12892	blood:	n/a	n/a
5	POLR2A	chr7:150906494-150907276	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr7:150907088-150907313	HCT-116	colon:	n/a	n/a
7	POLR2A	chr7:150907009-150907207	IMR90	lung:	n/a	n/a
8	POLR2A	chr7:150906054-150907466	K562	blood:	n/a	n/a
9	POLR2A	chr7:150906602-150907419	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:150906225-150907377	A549	lung:	n/a	n/a
11	POLR2A	chr7:150906969-150907472	GM12891	blood:	n/a	n/a
12	POLR2A	chr7:150906844-150907391	GM12891	blood:	n/a	n/a
13	POLR2A	chr7:150906955-150907445	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr7:150906053-150907258	GM12892	blood:	n/a	n/a
15	POLR2A	chr7:150906549-150910050	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr7:150903888-150910558	K562	blood:	n/a	n/a
17	POLR2A	chr7:150906959-150907442	HL-60	blood:	n/a	n/a
18	POLR2A	chr7:150904601-150907402	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr7:150906035-150907560	K562	blood:	n/a	n/a
20	POLR2A	chr7:150906487-150907376	K562	blood:	n/a	n/a
21	POLR2A	chr7:150906391-150910223	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr7:150906612-150907299	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:150893356..150896342-chr7:150905267..150908010,3	K562	blood:
2	chr7:150901201..150903051-chr7:150905841..150907689,2	MCF-7	breast:
3	chr7:150904819..150907851-chr7:150927889..150929495,3	MCF-7	breast:
4	chr7:150900947..150904902-chr7:150906819..150911270,6	MCF-7	breast:
5	chr7:150905577..150911406-chr7:150912646..150916801,5	MCF-7	breast:

No data

Variant related genes	Relation type
IQCA1P1	TF binding region
ENSG00000183016	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1065071	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10952299	1.00[CHB][hapmap]
rs11770520	1.00[CHB][hapmap]
rs12531871	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12538823	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1563636	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs219235	1.00[JPT][hapmap]
rs34129956	0.83[ASN][1000 genomes]
rs34770061	0.83[ASN][1000 genomes]
rs34821030	0.83[ASN][1000 genomes]
rs35093688	0.83[ASN][1000 genomes]
rs35302282	0.83[ASN][1000 genomes]
rs35833042	0.83[ASN][1000 genomes]
rs432519	1.00[CHB][hapmap]
rs66608097	0.83[ASN][1000 genomes]
rs7786151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv889476	chr7:150729212-150951819	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	120 gene(s)	inside rSNPs	diseases
3	nsv831188	chr7:150735204-150912875	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv609035	chr7:150896223-150955765	Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv971515	chr7:150905324-150908880	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6967282	GIMAP2	cis	cerebellum	SCAN
rs6967282	XRCC2	cis	cerebellum	SCAN
rs6967282	ABCF2	cis	brain	BrainEAC
rs6967282	CHPF2	cis	cerebellum	SCAN
rs6967282	ABCF2	cis	frontal cortex	BrainEAC
rs6967282	ABCF2	cis	hippocampus	BrainEAC

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150885000-150910000	Weak transcription	Right Atrium	heart
2	chr7:150899000-150909600	Weak transcription	Aorta	Aorta
3	chr7:150901800-150910000	Weak transcription	Ovary	ovary
4	chr7:150902000-150910200	Weak transcription	Right Ventricle	heart
5	chr7:150902000-150910400	Weak transcription	Pancreas	Pancrea
6	chr7:150903000-150908800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:150903200-150909600	Weak transcription	Spleen	Spleen
8	chr7:150904000-150909000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:150904200-150908000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:150904400-150909600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:150904600-150909600	Weak transcription	Psoas Muscle	Psoas
12	chr7:150904600-150909600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr7:150904800-150907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:150904800-150908600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:150904800-150908800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:150904800-150909200	Weak transcription	GM12878-XiMat	blood
17	chr7:150904800-150909400	Weak transcription	Fetal Thymus	thymus
18	chr7:150905000-150908200	Weak transcription	Primary T cells from cord blood	blood
19	chr7:150905000-150908400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:150905000-150910000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr7:150905000-150910000	Weak transcription	Esophagus	oesophagus
22	chr7:150905000-150910800	Weak transcription	Colonic Mucosa	Colon
23	chr7:150905200-150908000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:150905200-150908600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:150905200-150909200	Weak transcription	K562	blood
26	chr7:150905200-150909600	Weak transcription	Gastric	stomach
27	chr7:150905200-150910000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr7:150905200-150910200	Weak transcription	A549	lung
29	chr7:150905400-150908800	Weak transcription	Fetal Intestine Small	intestine
30	chr7:150905400-150909000	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:150905400-150909400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr7:150905400-150909600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:150905400-150912000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr7:150905400-150912000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr7:150905600-150909200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:150905600-150910000	Weak transcription	Brain Germinal Matrix	brain
37	chr7:150905600-150910000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr7:150905600-150911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr7:150905800-150908800	Weak transcription	Primary B cells from cord blood	blood
40	chr7:150905800-150908800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:150905800-150909000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:150905800-150909200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr7:150905800-150909200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr7:150905800-150909800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:150905800-150909800	Weak transcription	HMEC	breast
46	chr7:150905800-150910200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:150905800-150910200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:150905800-150910200	Weak transcription	HepG2	liver
49	chr7:150905800-150910800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:150906000-150908000	Weak transcription	Brain Hippocampus Middle	brain

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