Variant report

Variant	rs10875030
Chromosome Location	chr1:92339976-92339977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10493856	0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs10493857	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs10875033	0.97[ASN][1000 genomes]
rs10875037	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11165595	0.82[CEU][hapmap]
rs11165679	1.00[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs11165681	0.82[EUR][1000 genomes]
rs11165758	0.91[ASN][1000 genomes]
rs11165759	0.92[ASN][1000 genomes]
rs11165776	0.89[ASN][1000 genomes]
rs11580031	0.86[EUR][1000 genomes]
rs11580045	0.85[EUR][1000 genomes]
rs11590254	0.95[CEU][hapmap];0.87[TSI][hapmap]
rs1192524	1.00[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs12026798	0.89[EUR][1000 genomes]
rs12073180	0.92[ASN][1000 genomes]
rs12090417	0.92[ASN][1000 genomes]
rs12124897	0.84[CHB][hapmap]
rs12127774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141128	0.91[ASN][1000 genomes]
rs12142687	0.89[ASN][1000 genomes]
rs12566180	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12569180	1.00[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs12726500	0.82[CEU][hapmap]
rs12736904	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12747643	0.92[ASN][1000 genomes]
rs12749339	0.89[ASN][1000 genomes]
rs1488691	0.80[CHB][hapmap]
rs17516329	0.95[CEU][hapmap];0.87[TSI][hapmap]
rs17881430	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs2450924	0.84[EUR][1000 genomes]
rs2479870	0.90[ASN][1000 genomes]
rs2479871	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2489188	0.83[CEU][hapmap]
rs2770186	0.89[ASN][1000 genomes]
rs2770187	0.89[ASN][1000 genomes]
rs2799518	0.90[ASN][1000 genomes]
rs28403919	0.89[EUR][1000 genomes]
rs284147	0.86[CEU][hapmap]
rs284149	0.82[CEU][hapmap]
rs284153	0.82[CEU][hapmap]
rs284159	0.82[CEU][hapmap]
rs416624	0.82[CEU][hapmap]
rs61779066	0.87[EUR][1000 genomes]
rs6604061	0.84[CHB][hapmap]
rs6604064	0.91[ASN][1000 genomes]
rs6656018	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6680463	0.92[ASN][1000 genomes]
rs6680614	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6684753	0.80[CHB][hapmap]
rs7529166	0.80[ASN][1000 genomes]
rs7530354	0.92[ASN][1000 genomes]
rs7533784	0.81[ASN][1000 genomes]
rs7543879	0.92[ASN][1000 genomes]
rs7545838	0.85[EUR][1000 genomes]
rs7550028	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7555476	0.82[CEU][hapmap]
rs7555548	0.82[CEU][hapmap]
rs9661103	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
22	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv1002730	chr1:92302541-92565229	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv830581	chr1:92317207-92511175	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875030	GBP7	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92317400-92344400	Weak transcription	Fetal Intestine Large	intestine
2	chr1:92332400-92342400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:92335200-92343400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:92337400-92340000	Enhancers	Spleen	Spleen
5	chr1:92337400-92341200	Enhancers	Ovary	ovary
6	chr1:92338200-92342000	Weak transcription	Fetal Lung	lung
7	chr1:92338200-92342000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:92338400-92340600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:92338400-92340800	Weak transcription	Right Ventricle	heart
10	chr1:92338400-92341600	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:92338400-92341800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:92338400-92342000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:92338400-92342200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:92338400-92343800	Weak transcription	Fetal Kidney	kidney
15	chr1:92338400-92348600	Weak transcription	Right Atrium	heart
16	chr1:92338600-92340600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:92338600-92340600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:92338600-92341000	Weak transcription	Fetal Heart	heart
19	chr1:92338600-92341600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:92338600-92341800	Weak transcription	Osteobl	bone
21	chr1:92338600-92343200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:92338600-92343400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:92338600-92344400	Weak transcription	Fetal Intestine Small	intestine
24	chr1:92338600-92347200	Weak transcription	Psoas Muscle	Psoas
25	chr1:92338600-92348800	Weak transcription	Stomach Mucosa	stomach
26	chr1:92338600-92349600	Weak transcription	Pancreas	Pancrea
27	chr1:92338600-92350000	Weak transcription	Esophagus	oesophagus
28	chr1:92338600-92350000	Weak transcription	Left Ventricle	heart
29	chr1:92338800-92340400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:92338800-92341600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:92338800-92341600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:92338800-92341600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:92338800-92341600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:92338800-92341600	Weak transcription	NHLF	lung
35	chr1:92338800-92341800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:92338800-92341800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:92338800-92341800	Weak transcription	Fetal Stomach	stomach
38	chr1:92338800-92341800	Weak transcription	NHDF-Ad	bronchial
39	chr1:92338800-92342000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:92338800-92342600	Weak transcription	A549	lung
41	chr1:92338800-92343200	Weak transcription	Liver	Liver
42	chr1:92338800-92343200	Enhancers	HepG2	liver
43	chr1:92338800-92343600	Weak transcription	Hela-S3	cervix
44	chr1:92338800-92346800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:92338800-92350000	Weak transcription	K562	blood
46	chr1:92339000-92340200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:92339000-92340800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:92339000-92341800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:92339200-92340000	Bivalent Enhancer	Thymus	Thymus
50	chr1:92339200-92340600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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