Variant report

Variant	rs2163639
Chromosome Location	chr7:7195947-7195948
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10447684	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10487590	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs13238772	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13438509	0.90[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs17163878	0.80[CEU][hapmap]
rs17164011	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17249770	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17250084	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17251749	1.00[YRI][hapmap]
rs17309555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2116533	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2116534	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2116535	0.90[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2163638	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2881754	0.84[CEU][hapmap]
rs34386799	0.80[AMR][1000 genomes]
rs34419200	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34491888	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34705126	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34971257	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4324853	0.87[CEU][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4428582	0.87[EUR][1000 genomes]
rs4582461	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58312319	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58843310	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61465425	0.81[EUR][1000 genomes]
rs62449960	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62449964	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62449965	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62453487	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62453491	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62453504	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62453505	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62453506	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62453507	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62453510	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62453511	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62453512	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62453513	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6976254	1.00[CHD][hapmap]
rs9648103	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv428160	chr7:6936949-7219553	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1020929	chr7:6954959-7232920	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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	39 gene(s)	inside rSNPs	diseases
6	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
7	nsv887469	chr7:7036939-7205749	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv1015553	chr7:7053923-7201291	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv538719	chr7:7053923-7201291	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2163639	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL
rs2163639	C1GALT1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7188800-7196400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:7188800-7196400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:7189000-7196800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:7189200-7199600	Weak transcription	K562	blood
5	chr7:7189600-7196400	Weak transcription	Stomach Mucosa	stomach
6	chr7:7191400-7196200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:7191800-7196400	Weak transcription	Thymus	Thymus
8	chr7:7195000-7196400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr7:7195200-7196400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr7:7195200-7196400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr7:7195200-7196600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:7195200-7196800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr7:7195400-7196200	Enhancers	Primary T cells from cord blood	blood
14	chr7:7195400-7196200	Enhancers	Dnd41	blood
15	chr7:7195400-7196400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:7195400-7196400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr7:7195400-7196800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:7195600-7196200	Enhancers	Osteobl	bone
19	chr7:7195600-7196400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr7:7195600-7196400	Enhancers	HepG2	liver
21	chr7:7195600-7196400	Enhancers	HSMMtube	muscle
22	chr7:7195600-7196600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:7195600-7196600	Enhancers	Primary B cells from cord blood	blood
24	chr7:7195600-7196600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr7:7195600-7196600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr7:7195600-7196800	Enhancers	Primary B cells from peripheral blood	blood
27	chr7:7195600-7196800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr7:7195600-7196800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:7195600-7196800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:7195800-7196000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr7:7195800-7196400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:7195800-7196400	Enhancers	HSMM	muscle
33	chr7:7195800-7196800	Enhancers	HMEC	breast
34	chr7:7195800-7197000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:7195800-7197000	Enhancers	GM12878-XiMat	blood

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