Variant report

Variant	rs9730180
Chromosome Location	chr1:180475079-180475080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:180474982-180475478	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:180474916-180475480	MCF10A-Er-Src	breast:	n/a	chr1:180475268-180475279 chr1:180475270-180475278
3	STAT3	chr1:180474992-180475538	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:180475024-180475451	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:180474883-180475453	MCF10A-Er-Src	breast:	n/a	chr1:180475268-180475279 chr1:180475270-180475278
6	FOS	chr1:180474852-180475499	MCF10A-Er-Src	breast:	n/a	chr1:180475268-180475279 chr1:180475270-180475278
7	FOS	chr1:180475072-180475477	HUVEC	blood vessel:	n/a	chr1:180475268-180475279 chr1:180475270-180475278
8	FOS	chr1:180475011-180475478	MCF10A-Er-Src	breast:	n/a	chr1:180475268-180475279 chr1:180475270-180475278

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180469977..180474881-chr1:180475033..180479240,11	K562	blood:

Variant related genes	Relation type
ACBD6	TF binding region
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10158367	0.88[ASN][1000 genomes]
rs10465516	0.83[ASN][1000 genomes]
rs10494527	0.84[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10753208	0.84[ASN][1000 genomes]
rs10753209	0.89[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10753211	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10753212	0.89[ASN][1000 genomes]
rs10798745	0.85[CHB][hapmap]
rs10798746	0.90[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs10798756	0.86[ASN][1000 genomes]
rs10798757	0.86[ASN][1000 genomes]
rs10798759	0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10798760	0.86[ASN][1000 genomes]
rs10798762	0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10798766	0.87[ASN][1000 genomes]
rs10798769	0.80[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10798770	0.92[ASN][1000 genomes]
rs10798771	0.91[ASN][1000 genomes]
rs10913968	0.83[ASN][1000 genomes]
rs10913969	0.90[CHB][hapmap]
rs10913973	0.83[ASN][1000 genomes]
rs10913974	0.86[ASN][1000 genomes]
rs10913976	0.86[ASN][1000 genomes]
rs10913978	0.86[ASN][1000 genomes]
rs10913980	0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10913981	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs10913982	0.86[ASN][1000 genomes]
rs10913983	0.86[ASN][1000 genomes]
rs10913984	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs10913985	0.89[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10913986	0.86[ASN][1000 genomes]
rs10913987	0.86[ASN][1000 genomes]
rs10913994	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10913998	0.88[ASN][1000 genomes]
rs10914001	0.89[ASN][1000 genomes]
rs10914005	0.80[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10914010	0.87[ASN][1000 genomes]
rs10914014	0.93[ASN][1000 genomes]
rs10914016	0.90[ASN][1000 genomes]
rs10914017	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10914018	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs11580793	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11799870	0.84[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12034217	0.90[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs12034669	0.81[ASN][1000 genomes]
rs12039933	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12041620	0.88[EUR][1000 genomes]
rs12045123	0.81[ASN][1000 genomes]
rs12085808	0.81[ASN][1000 genomes]
rs12091722	0.89[CHB][hapmap]
rs12121043	0.90[ASN][1000 genomes]
rs12122338	0.86[ASN][1000 genomes]
rs12127886	0.89[ASN][1000 genomes]
rs12128560	0.85[ASN][1000 genomes]
rs12129511	0.86[ASN][1000 genomes]
rs12129784	0.86[ASN][1000 genomes]
rs12131071	0.89[ASN][1000 genomes]
rs12132837	0.88[ASN][1000 genomes]
rs12135463	0.89[ASN][1000 genomes]
rs12141348	0.84[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12141848	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12143350	0.84[ASN][1000 genomes]
rs12404209	0.90[CHB][hapmap]
rs12405902	0.90[CHB][hapmap]
rs12407122	0.81[ASN][1000 genomes]
rs12561776	0.83[ASN][1000 genomes]
rs12565492	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs12730889	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs12733492	0.90[ASN][1000 genomes]
rs1341924	0.89[CHB][hapmap]
rs1416821	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1416823	0.89[CHB][hapmap]
rs1538620	0.89[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs16856086	0.88[EUR][1000 genomes]
rs1890731	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1970400	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2105232	0.92[ASN][1000 genomes]
rs2296378	0.81[ASN][1000 genomes]
rs28506072	0.83[ASN][1000 genomes]
rs2877415	0.90[CHB][hapmap]
rs3737584	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs3806300	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3806301	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3923222	0.86[ASN][1000 genomes]
rs4076403	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4142992	0.88[ASN][1000 genomes]
rs4418555	0.88[ASN][1000 genomes]
rs4420052	0.88[ASN][1000 genomes]
rs4421553	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs4442335	0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4543756	0.89[CHB][hapmap]
rs4578179	0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4607831	0.89[ASN][1000 genomes]
rs4634864	0.86[ASN][1000 genomes]
rs4651064	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs4652504	0.83[ASN][1000 genomes]
rs4652505	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs60286873	0.82[ASN][1000 genomes]
rs6425634	0.90[CHB][hapmap]
rs6425641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425644	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6665719	0.90[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs6670544	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6674244	0.89[ASN][1000 genomes]
rs6687442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687549	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697924	0.81[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6699585	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6700986	0.89[ASN][1000 genomes]
rs6704334	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];0.99[ASN][1000 genomes]
rs6704437	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];0.99[ASN][1000 genomes]
rs72720915	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72720917	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72720922	0.86[EUR][1000 genomes]
rs7521151	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7523003	0.86[ASN][1000 genomes]
rs7523857	0.89[ASN][1000 genomes]
rs7528650	0.89[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7532806	0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9701037	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9726041	0.91[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]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
7	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180472400-180477600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:180472400-180481400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:180472600-180477000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:180472800-180475200	Weak transcription	NH-A	brain
5	chr1:180472800-180477200	Weak transcription	Brain Substantia Nigra	brain
6	chr1:180472800-180488800	Weak transcription	Right Atrium	heart
7	chr1:180473000-180475200	Weak transcription	A549	lung
8	chr1:180473000-180476800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:180473000-180476800	Weak transcription	K562	blood
10	chr1:180473000-180477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:180473600-180475200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:180473600-180475200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:180473600-180475800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:180473600-180477000	Weak transcription	HMEC	breast
15	chr1:180474200-180475400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:180474400-180475400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:180474400-180475600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:180474400-180477800	Enhancers	HUVEC	blood vessel
19	chr1:180474800-180475600	Enhancers	Hela-S3	cervix
20	chr1:180474800-180481800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:180475000-180475200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:180475000-180475200	Enhancers	Brain Anterior Caudate	brain
23	chr1:180475000-180475400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:180475000-180475400	Enhancers	NHDF-Ad	bronchial
25	chr1:180475000-180475400	Flanking Active TSS	Osteobl	bone
26	chr1:180475000-180475600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:180475000-180475600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:180475000-180475800	Enhancers	NHLF	lung

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