Variant report

Variant	rs6676989
Chromosome Location	chr1:180028741-180028742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179849763..179851404-chr1:180027993..180029985,2	K562	blood:
2	chr1:180007479..180009332-chr1:180027865..180030769,2	K562	blood:
3	chr1:180023147..180025587-chr1:180027128..180029217,2	K562	blood:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10913916	0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10913917	0.80[JPT][hapmap]
rs10913918	0.84[CEU][hapmap]
rs10913927	0.93[JPT][hapmap]
rs12075450	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs12091685	0.81[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12094391	0.81[EUR][1000 genomes]
rs16855164	0.97[ASN][1000 genomes]
rs1981314	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2319676	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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2319677	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs2319773	0.91[ASN][1000 genomes]
rs2477106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2477107	0.87[ASN][1000 genomes]
rs2477109	0.85[ASN][1000 genomes]
rs2477111	0.80[JPT][hapmap]
rs2477112	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2477113	0.83[ASN][1000 genomes]
rs2477115	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2477117	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2477118	0.80[JPT][hapmap]
rs2477119	0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2483622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2501608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2501611	0.80[JPT][hapmap]
rs2501613	0.80[JPT][hapmap]
rs2501614	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2501615	0.80[JPT][hapmap]
rs2501618	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2501619	0.82[ASN][1000 genomes]
rs2501621	0.93[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2762859	0.80[JPT][hapmap]
rs3123521	0.89[ASN][1000 genomes]
rs3767201	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs3818999	0.80[JPT][hapmap]
rs3930305	0.93[JPT][hapmap]
rs4076449	0.93[JPT][hapmap]
rs4147170	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs4256775	0.93[JPT][hapmap]
rs4263962	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4379644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4622030	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs4651055	0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4652461	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4652464	0.91[ASN][1000 genomes]
rs4652465	0.93[JPT][hapmap]
rs483307	0.80[JPT][hapmap]
rs510209	0.80[JPT][hapmap]
rs551607	0.81[ASW][hapmap]
rs552743	0.84[CEU][hapmap]
rs55953436	0.89[EUR][1000 genomes]
rs55971224	0.88[EUR][1000 genomes]
rs6425602	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425603	0.93[JPT][hapmap]
rs6425606	0.90[ASW][hapmap];0.89[CEU][hapmap];0.85[JPT][hapmap]
rs6425607	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs6657347	0.93[JPT][hapmap]
rs6659911	0.97[ASN][1000 genomes]
rs6660984	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6682558	0.88[CEU][hapmap]
rs6692394	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7521948	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7547954	0.83[EUR][1000 genomes]
rs9286932	0.93[JPT][hapmap]
rs9425849	0.93[JPT][hapmap]
rs9425852	0.96[ASN][1000 genomes]
rs9425853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425854	0.93[JPT][hapmap]
rs9425857	0.95[ASN][1000 genomes]
rs9425858	0.90[ASN][1000 genomes]
rs9425859	0.91[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9425861	0.93[JPT][hapmap]
rs9887843	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv3755	chr1:179998860-180043554	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv1000698	chr1:179999669-180042521	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
15	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
16	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
2	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:179976200-180063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:179981000-180059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:179989800-180034200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:179992400-180031400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:179992400-180032200	Weak transcription	Esophagus	oesophagus
9	chr1:180000200-180029200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:180000600-180039800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:180009000-180041200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr1:180009000-180069600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:180009200-180051800	Strong transcription	Fetal Thymus	thymus
16	chr1:180009200-180070000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:180010200-180029000	Strong transcription	Primary B cells from cord blood	blood
18	chr1:180010200-180040400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:180010200-180052000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:180010600-180051800	Strong transcription	Liver	Liver
21	chr1:180012400-180031600	Weak transcription	Gastric	stomach
22	chr1:180012800-180050400	Weak transcription	Stomach Mucosa	stomach
23	chr1:180013000-180031800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:180013000-180080000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:180014600-180031600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:180016000-180031600	Weak transcription	Right Ventricle	heart
27	chr1:180016400-180049600	Weak transcription	NHEK	skin
28	chr1:180020000-180036400	Weak transcription	Fetal Brain Male	brain
29	chr1:180020800-180031600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:180021200-180031400	Weak transcription	NHLF	lung
31	chr1:180021400-180031600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:180021400-180062200	Weak transcription	Fetal Heart	heart
33	chr1:180023000-180031000	Weak transcription	Colonic Mucosa	Colon
34	chr1:180023400-180031200	Weak transcription	NH-A	brain
35	chr1:180023600-180031400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:180023600-180031600	Weak transcription	HepG2	liver
37	chr1:180023800-180030600	Weak transcription	HMEC	breast
38	chr1:180023800-180031400	Weak transcription	Fetal Kidney	kidney
39	chr1:180023800-180031400	Weak transcription	HSMMtube	muscle
40	chr1:180023800-180031600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:180023800-180031600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:180023800-180031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:180024000-180031200	Weak transcription	Brain Germinal Matrix	brain
44	chr1:180024000-180031400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:180024200-180031000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:180024400-180030800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:180024400-180031400	Weak transcription	Brain Anterior Caudate	brain
48	chr1:180024600-180029200	Weak transcription	Brain Substantia Nigra	brain
49	chr1:180024600-180030800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:180024600-180030800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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