Variant report

Variant	rs6426100
Chromosome Location	chr1:224467117-224467118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10158063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10733024	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10737442	0.81[ASN][1000 genomes]
rs10753462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10753464	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10799562	0.81[ASW][hapmap];0.85[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10799563	0.81[ASN][1000 genomes]
rs10916585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs11802486	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs16846031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs16846094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs16846214	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16846244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1806742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2001712	0.81[ASN][1000 genomes]
rs2404783	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2404857	0.81[AFR][1000 genomes]
rs2404858	0.81[ASN][1000 genomes]
rs2404859	0.81[ASN][1000 genomes]
rs2404861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2405062	0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2405065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap]
rs2896990	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs2896992	0.81[ASN][1000 genomes]
rs2897054	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3754090	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3767721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs3767722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs3767723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs3767724	0.81[ASN][1000 genomes]
rs3767725	0.81[ASN][1000 genomes]
rs4146965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4146966	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4233234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs4233235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs4256779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap]
rs4420060	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4653575	0.81[ASN][1000 genomes]
rs4653579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs4653580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs4653581	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs4653584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4654011	0.84[AMR][1000 genomes]
rs4654013	0.85[JPT][hapmap]
rs4654017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4654019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs4654022	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs4654023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs55675086	0.86[ASN][1000 genomes]
rs55980628	0.81[ASN][1000 genomes]
rs57324770	0.81[ASN][1000 genomes]
rs58855990	0.81[ASN][1000 genomes]
rs6426088	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs6426094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6426110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6426117	0.81[ASN][1000 genomes]
rs6681790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap]
rs6682667	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6694745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs6696795	0.81[ASN][1000 genomes]
rs6699017	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73118046	0.81[ASN][1000 genomes]
rs73128468	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73130436	0.81[ASN][1000 genomes]
rs73130448	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73130455	0.81[ASN][1000 genomes]
rs73130462	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73130464	0.81[ASN][1000 genomes]
rs7521015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7522392	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7529143	0.81[ASN][1000 genomes]
rs7530205	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7534101	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs7534447	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9287027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
2	chr1:224412400-224473600	Weak transcription	HepG2	liver
3	chr1:224424600-224479600	Weak transcription	Pancreas	Pancrea
4	chr1:224425600-224470000	Weak transcription	NHDF-Ad	bronchial
5	chr1:224431200-224490400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:224433400-224516200	Weak transcription	Fetal Heart	heart
7	chr1:224434400-224474800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:224434400-224474800	Weak transcription	Fetal Brain Male	brain
9	chr1:224436800-224473600	Weak transcription	Gastric	stomach
10	chr1:224437000-224475200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:224437000-224476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:224437000-224479600	Weak transcription	Right Ventricle	heart
13	chr1:224437600-224474800	Weak transcription	Colonic Mucosa	Colon
14	chr1:224438000-224474600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:224439800-224501600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:224440400-224474800	Weak transcription	Fetal Kidney	kidney
17	chr1:224444600-224479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:224445400-224482000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:224446000-224470600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:224450400-224470000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:224450600-224473600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:224450800-224472200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:224450800-224480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:224451000-224469800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:224452400-224469200	Weak transcription	Aorta	Aorta
26	chr1:224452800-224472400	Weak transcription	Brain Germinal Matrix	brain
27	chr1:224454800-224475400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:224454800-224480000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:224455000-224472200	Weak transcription	HSMMtube	muscle
30	chr1:224455000-224474800	Weak transcription	Ovary	ovary
31	chr1:224455000-224480200	Weak transcription	Psoas Muscle	Psoas
32	chr1:224456000-224474600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:224456200-224469800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:224456400-224470200	Weak transcription	HMEC	breast
35	chr1:224457200-224479600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:224457600-224469200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:224458000-224468000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:224459400-224467400	Weak transcription	GM12878-XiMat	blood
39	chr1:224461000-224469000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:224461200-224505600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:224461600-224475400	Weak transcription	Lung	lung
42	chr1:224462000-224473800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:224462200-224467600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:224462200-224468000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:224462200-224479600	Weak transcription	Spleen	Spleen
46	chr1:224462400-224469000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:224462800-224468600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:224462800-224470000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:224463000-224468000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:224463000-224468000	Weak transcription	Fetal Thymus	thymus

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