Variant report

Variant	rs6659911
Chromosome Location	chr1:180034602-180034603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179994934..179997849-chr1:180033158..180035390,2	MCF-7	breast:
2	chr1:180032822..180035460-chr1:180037133..180039107,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10798729	0.80[JPT][hapmap]
rs10913916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913917	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10913927	0.93[JPT][hapmap]
rs12075450	0.80[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs16855164	0.96[ASN][1000 genomes]
rs1981314	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[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];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2319676	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2319677	0.86[JPT][hapmap]
rs2319773	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2477106	0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2477107	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2477109	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2477111	0.81[JPT][hapmap]
rs2477112	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs2477113	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2477115	0.82[ASN][1000 genomes]
rs2477117	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2477118	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2477119	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2483622	0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2501607	0.82[CHB][hapmap]
rs2501608	0.93[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2501611	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2501613	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2501614	0.85[ASN][1000 genomes]
rs2501615	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2501618	0.84[ASN][1000 genomes]
rs2501619	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2501621	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2762859	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3123521	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767201	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs3818999	0.81[JPT][hapmap]
rs3930305	0.93[JPT][hapmap]
rs4076449	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs4147170	0.86[JPT][hapmap]
rs4256775	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs4263962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4379644	0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4622030	0.86[JPT][hapmap]
rs4651055	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652461	0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs4652464	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652465	0.93[JPT][hapmap]
rs483307	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs510209	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6425602	0.91[ASN][1000 genomes]
rs6425603	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs6425606	0.85[JPT][hapmap]
rs6425607	0.86[JPT][hapmap]
rs6657347	0.93[JPT][hapmap]
rs6660984	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6676989	0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6692394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7412536	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7521948	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7544467	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7545835	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9286932	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs9425483	0.83[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs9425849	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs9425852	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425853	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425854	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs9425857	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425858	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425859	0.88[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425861	0.93[JPT][hapmap]
rs9887843	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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
18	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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
20	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:179976200-180063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:179981000-180059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:180000600-180039800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:180009000-180041200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr1:180009000-180069600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:180009200-180051800	Strong transcription	Fetal Thymus	thymus
11	chr1:180009200-180070000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:180010200-180040400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:180010200-180052000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:180010600-180051800	Strong transcription	Liver	Liver
15	chr1:180012800-180050400	Weak transcription	Stomach Mucosa	stomach
16	chr1:180013000-180080000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:180016400-180049600	Weak transcription	NHEK	skin
18	chr1:180020000-180036400	Weak transcription	Fetal Brain Male	brain
19	chr1:180021400-180062200	Weak transcription	Fetal Heart	heart
20	chr1:180025000-180064800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:180025600-180039400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:180027000-180050000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:180028000-180037800	Strong transcription	GM12878-XiMat	blood
24	chr1:180028200-180037000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:180028600-180052200	Strong transcription	Dnd41	blood
26	chr1:180029400-180035000	Strong transcription	Fetal Intestine Small	intestine
27	chr1:180029400-180035200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:180029400-180035200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:180029400-180037200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:180029600-180084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:180030000-180035000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:180030000-180073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:180030200-180035000	Strong transcription	Fetal Stomach	stomach
34	chr1:180030200-180037400	Strong transcription	Fetal Intestine Large	intestine
35	chr1:180030200-180039800	Strong transcription	NHDF-Ad	bronchial
36	chr1:180030200-180040200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:180030200-180041800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:180030400-180034800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:180030400-180035000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:180030400-180035000	Strong transcription	Ovary	ovary
41	chr1:180030400-180035200	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:180030400-180035400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:180030400-180038000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:180030400-180039400	Strong transcription	HSMM	muscle
45	chr1:180030400-180040000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:180030400-180040000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:180030400-180066600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:180030600-180039600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:180030600-180040000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:180030800-180035000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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