Variant report

Variant	rs6960962
Chromosome Location	chr7:7258339-7258340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7258238..7260698-chr7:7260877..7262796,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10278474	0.81[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10487590	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs12667853	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs5010182	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs55637396	0.82[ASN][1000 genomes]
rs73043785	0.85[ASN][1000 genomes]
rs73043789	0.82[ASN][1000 genomes]
rs73045769	0.91[ASN][1000 genomes]
rs73045773	0.88[ASN][1000 genomes]
rs73049974	0.84[ASN][1000 genomes]
rs73049983	0.84[ASN][1000 genomes]
rs73049994	0.82[ASN][1000 genomes]
rs73049999	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1023133	chr7:6854098-7516700	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv464300	chr7:7040176-7368699	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv606033	chr7:7040176-7368699	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1016369	chr7:7053923-7375567	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1023788	chr7:7053923-7407783	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv538720	chr7:7053923-7407783	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
10	nsv1032813	chr7:7053923-7497484	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
13	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv1032974	chr7:7145831-7393218	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
16	nsv508445	chr7:7190518-7261098	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	esv2758102	chr7:7209911-7493901	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
18	esv2759505	chr7:7209911-7493901	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	nsv464301	chr7:7252775-7442169	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
20	nsv606035	chr7:7252775-7442169	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6960962	RAC1	cis	parietal	SCAN
rs6960962	GLCCI1	cis	cerebellum	SCAN
rs6960962	C1GALT1	cis	parietal	SCAN
rs6960962	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL
rs6960962	C1GALT1	cis	cerebellum	SCAN
rs6960962	C1GALT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7223800-7279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:7241600-7263000	Weak transcription	Right Atrium	heart
3	chr7:7241600-7273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:7242000-7261200	Weak transcription	Stomach Mucosa	stomach
5	chr7:7242000-7261400	Weak transcription	Right Ventricle	heart
6	chr7:7242200-7260400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:7246600-7260400	Weak transcription	NHDF-Ad	bronchial
8	chr7:7247600-7275000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:7247800-7267400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:7248600-7261400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:7248600-7263200	Weak transcription	Gastric	stomach
12	chr7:7250800-7260600	Weak transcription	Hela-S3	cervix
13	chr7:7250800-7261400	Weak transcription	Pancreas	Pancrea
14	chr7:7250800-7296600	Weak transcription	Spleen	Spleen
15	chr7:7251000-7261000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:7251600-7261400	Weak transcription	Brain Germinal Matrix	brain
17	chr7:7252200-7258400	Strong transcription	Primary T cells from cord blood	blood
18	chr7:7252400-7261200	Weak transcription	NHLF	lung
19	chr7:7252600-7261200	Weak transcription	Small Intestine	intestine
20	chr7:7252600-7273000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:7252800-7258800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr7:7252800-7260800	Weak transcription	A549	lung
23	chr7:7253000-7276800	Weak transcription	Fetal Heart	heart
24	chr7:7253600-7259000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:7253800-7258400	Strong transcription	Fetal Intestine Large	intestine
26	chr7:7253800-7258400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr7:7253800-7258800	Strong transcription	Placenta	Placenta
28	chr7:7253800-7259000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:7254000-7258400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:7254200-7258400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:7254200-7258400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr7:7254200-7258400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr7:7254200-7258800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr7:7254200-7259000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr7:7254200-7259200	Strong transcription	HSMM	muscle
36	chr7:7254400-7258400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr7:7254400-7258400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:7254400-7258400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:7254400-7258400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:7254400-7258600	Strong transcription	Primary B cells from cord blood	blood
41	chr7:7254400-7259000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:7254600-7258400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:7254600-7259000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:7254800-7261400	Weak transcription	Esophagus	oesophagus
45	chr7:7255000-7260600	Weak transcription	HUVEC	blood vessel
46	chr7:7255000-7261200	Weak transcription	Aorta	Aorta
47	chr7:7255000-7261400	Weak transcription	Left Ventricle	heart
48	chr7:7255000-7266200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr7:7255200-7258600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:7255200-7261400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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