Variant report

Variant	rs13246962
Chromosome Location	chr7:7252775-7252776
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	chr7:7252566..7255017-chr7:7255742..7257281,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10225975	0.85[AMR][1000 genomes]
rs10256877	0.84[AMR][1000 genomes]
rs10272173	0.85[AMR][1000 genomes]
rs10277583	0.82[AMR][1000 genomes]
rs10447684	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10487590	1.00[CHD][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes]
rs13222351	0.89[AMR][1000 genomes]
rs13234717	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13238772	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13438509	1.00[CHD][hapmap]
rs17164166	0.82[YRI][hapmap]
rs17249770	0.80[EUR][1000 genomes]
rs17250084	0.81[EUR][1000 genomes]
rs17251749	0.82[AMR][1000 genomes]
rs2116533	1.00[CHD][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2116534	0.80[EUR][1000 genomes]
rs2116535	0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2163638	0.81[EUR][1000 genomes]
rs2163639	1.00[CHD][hapmap]
rs34386799	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34419200	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34491888	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34705126	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34971257	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4324853	0.80[EUR][1000 genomes]
rs4582461	1.00[CHD][hapmap];0.87[TSI][hapmap]
rs62449960	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62449964	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62449965	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62450007	0.84[AMR][1000 genomes]
rs62453491	0.80[EUR][1000 genomes]
rs62453507	0.81[EUR][1000 genomes]
rs6976254	1.00[CHD][hapmap]
rs9648103	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][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
rs13246962	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL
rs13246962	COL28A1	cis	parietal	SCAN
rs13246962	C1GALT1	cis	parietal	SCAN
rs13246962	RAC1	cis	parietal	SCAN
rs13246962	GLCCI1	cis	cerebellum	SCAN
rs13246962	C1GALT1	cis	cerebellum	SCAN

Chromatin state (count:105 , 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	chr7:7241200-7254400	Weak transcription	Aorta	Aorta
3	chr7:7241400-7254400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:7241600-7257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:7241600-7263000	Weak transcription	Right Atrium	heart
6	chr7:7241600-7273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:7241800-7253800	Weak transcription	Placenta	Placenta
8	chr7:7241800-7254400	Weak transcription	Thymus	Thymus
9	chr7:7242000-7254400	Weak transcription	Esophagus	oesophagus
10	chr7:7242000-7254400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:7242000-7261200	Weak transcription	Stomach Mucosa	stomach
12	chr7:7242000-7261400	Weak transcription	Right Ventricle	heart
13	chr7:7242200-7260400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:7243800-7254200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:7244000-7254400	Weak transcription	Liver	Liver
16	chr7:7244200-7256400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:7244600-7254200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:7245000-7254200	Weak transcription	Dnd41	blood
19	chr7:7246200-7255800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:7246600-7260400	Weak transcription	NHDF-Ad	bronchial
21	chr7:7247200-7253000	Weak transcription	Osteobl	bone
22	chr7:7247600-7275000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:7247800-7254400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:7247800-7255600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr7:7247800-7267400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:7248000-7254400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:7248400-7254200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:7248400-7254200	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:7248600-7254200	Weak transcription	GM12878-XiMat	blood
30	chr7:7248600-7254200	Weak transcription	NHEK	skin
31	chr7:7248600-7257200	Weak transcription	HMEC	breast
32	chr7:7248600-7261400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:7248600-7263200	Weak transcription	Gastric	stomach
34	chr7:7248800-7253000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:7249000-7254800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:7249200-7253400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:7249200-7255600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr7:7249400-7254200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr7:7249400-7254400	Weak transcription	Ovary	ovary
40	chr7:7249400-7254400	Weak transcription	K562	blood
41	chr7:7249600-7255000	Weak transcription	Fetal Thymus	thymus
42	chr7:7250000-7255800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:7250200-7254400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr7:7250400-7254000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr7:7250400-7254200	Weak transcription	Fetal Stomach	stomach
46	chr7:7250400-7256800	Weak transcription	Fetal Brain Female	brain
47	chr7:7250600-7254400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr7:7250600-7254800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:7250800-7253600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:7250800-7253800	Weak transcription	Monocytes-CD14+_RO01746	blood

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