Variant report

Variant	rs2129975
Chromosome Location	chr1:92282080-92282081
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1017956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1017957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10493856	0.83[MEX][hapmap]
rs10493858	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs10783036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783040	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10874976	0.96[YRI][hapmap]
rs10874981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874983	0.86[ASN][1000 genomes]
rs10874996	0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs10875001	0.83[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs11165532	0.96[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11165560	0.87[ASN][1000 genomes]
rs11165587	0.82[ASN][1000 genomes]
rs11165594	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs11466573	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12089918	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12124897	0.82[JPT][hapmap]
rs12132114	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12133180	0.83[ASN][1000 genomes]
rs1411276	0.82[YRI][hapmap]
rs2046739	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2297142	0.95[YRI][hapmap]
rs2489190	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2634031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2799537	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658276	0.87[ASN][1000 genomes]
rs5019497	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6604056	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6604060	0.82[JPT][hapmap]
rs6604061	0.82[JPT][hapmap]
rs6684753	0.82[JPT][hapmap]
rs6686126	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6691098	0.86[YRI][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2129975	GFI1	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92264800-92284200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:92272200-92282600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:92272400-92285400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:92275200-92284200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:92275400-92283200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:92275600-92283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:92275600-92292000	Weak transcription	Lung	lung
8	chr1:92276000-92284000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:92276400-92285000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:92277400-92291800	Enhancers	HepG2	liver
11	chr1:92277800-92282600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:92277800-92283000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:92277800-92283200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:92277800-92283200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:92277800-92286600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:92278000-92282800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:92278000-92283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:92278000-92285200	Weak transcription	Brain Substantia Nigra	brain
19	chr1:92278800-92288200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:92279400-92283000	Weak transcription	Fetal Thymus	thymus
21	chr1:92279600-92283000	Weak transcription	Placenta	Placenta
22	chr1:92279600-92284600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:92279600-92284600	Weak transcription	Left Ventricle	heart
24	chr1:92279600-92285000	Weak transcription	Esophagus	oesophagus
25	chr1:92279600-92285000	Weak transcription	Right Ventricle	heart
26	chr1:92279600-92287000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:92279600-92287200	Weak transcription	Spleen	Spleen
28	chr1:92279600-92294000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:92279800-92283600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:92279800-92284200	Weak transcription	Right Atrium	heart
31	chr1:92280200-92285000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:92280600-92286600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:92280800-92283200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:92280800-92284400	Weak transcription	Hela-S3	cervix
35	chr1:92281000-92284800	Enhancers	Liver	Liver
36	chr1:92281000-92285600	Enhancers	Adipose Nuclei	Adipose
37	chr1:92281000-92285800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:92281000-92285800	Enhancers	Colon Smooth Muscle	Colon
39	chr1:92281000-92285800	Enhancers	Fetal Kidney	kidney
40	chr1:92281200-92286600	Enhancers	Fetal Heart	heart
41	chr1:92281200-92286600	Enhancers	Rectal Smooth Muscle	rectum
42	chr1:92281400-92282200	Enhancers	Fetal Intestine Large	intestine
43	chr1:92281400-92282200	Enhancers	Fetal Intestine Small	intestine
44	chr1:92281400-92282200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:92281400-92284000	Enhancers	NHDF-Ad	bronchial
46	chr1:92281400-92285600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:92281400-92285600	Enhancers	Fetal Lung	lung
48	chr1:92281600-92282600	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:92281600-92282800	Weak transcription	Brain Anterior Caudate	brain
50	chr1:92281600-92283200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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