Variant report

Variant	rs946635
Chromosome Location	chr1:180493304-180493305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180491628..180493840-chr1:180599404..180602125,2	MCF-7	breast:
2	chr1:180491568..180494207-chr1:180499661..180501962,2	MCF-7	breast:
3	chr1:180491722..180497520-chr1:180497939..180503107,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10157891	0.87[EUR][1000 genomes]
rs10733004	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10737343	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10737344	0.87[EUR][1000 genomes]
rs10737345	0.91[EUR][1000 genomes]
rs10753213	0.87[EUR][1000 genomes]
rs10798749	0.85[EUR][1000 genomes]
rs10798763	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10798764	0.87[EUR][1000 genomes]
rs10913972	0.87[EUR][1000 genomes]
rs10914011	0.91[EUR][1000 genomes]
rs1094597	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1094598	0.87[EUR][1000 genomes]
rs1094599	0.87[EUR][1000 genomes]
rs12027553	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12144149	0.87[EUR][1000 genomes]
rs12565152	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs1339722	0.91[EUR][1000 genomes]
rs1339723	0.91[EUR][1000 genomes]
rs1361628	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1418100	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1418103	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1556935	0.91[EUR][1000 genomes]
rs1556938	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs1591898	0.87[EUR][1000 genomes]
rs17300950	0.86[JPT][hapmap]
rs1934411	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1961741	0.91[EUR][1000 genomes]
rs2153753	0.82[CEU][hapmap]
rs2262371	0.91[EUR][1000 genomes]
rs2331739	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs2764434	0.83[EUR][1000 genomes]
rs2764435	0.91[EUR][1000 genomes]
rs2764436	0.91[EUR][1000 genomes]
rs2764437	0.85[EUR][1000 genomes]
rs2764438	0.91[EUR][1000 genomes]
rs2764439	0.87[EUR][1000 genomes]
rs2764440	0.87[EUR][1000 genomes]
rs2764441	0.87[EUR][1000 genomes]
rs2764442	0.87[EUR][1000 genomes]
rs2764444	0.91[EUR][1000 genomes]
rs2794975	0.85[EUR][1000 genomes]
rs2794976	0.87[EUR][1000 genomes]
rs4259605	1.00[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs4281291	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4304539	0.87[EUR][1000 genomes]
rs4333819	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4532796	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs4540612	0.87[EUR][1000 genomes]
rs4651061	0.87[EUR][1000 genomes]
rs4651063	1.00[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs4651066	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs4652502	0.87[EUR][1000 genomes]
rs6425620	0.87[EUR][1000 genomes]
rs6425621	0.87[EUR][1000 genomes]
rs6425622	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6425623	0.91[EUR][1000 genomes]
rs6425624	0.83[EUR][1000 genomes]
rs6425626	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6425630	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6425642	0.91[EUR][1000 genomes]
rs6425647	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6659147	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6664944	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6665615	0.91[EUR][1000 genomes]
rs6669304	0.87[EUR][1000 genomes]
rs6677367	0.87[EUR][1000 genomes]
rs6678261	0.85[EUR][1000 genomes]
rs6680754	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6683484	0.91[EUR][1000 genomes]
rs6687873	0.87[EUR][1000 genomes]
rs6691333	0.87[EUR][1000 genomes]
rs6695360	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7515052	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs7522928	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7526743	0.87[EUR][1000 genomes]
rs7530015	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7532972	0.87[EUR][1000 genomes]
rs7542568	0.85[EUR][1000 genomes]
rs7546030	0.87[EUR][1000 genomes]
rs7548707	0.91[EUR][1000 genomes]
rs7555087	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs822704	1.00[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs822705	1.00[CEU][hapmap]
rs863720	0.85[EUR][1000 genomes]
rs863721	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs946633	0.89[EUR][1000 genomes]
rs946634	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180486000-180493400	Weak transcription	Fetal Stomach	stomach
2	chr1:180486000-180499400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:180486400-180493800	Weak transcription	Fetal Lung	lung
4	chr1:180488000-180500400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:180488600-180497000	Enhancers	Placenta	Placenta
6	chr1:180489400-180494400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:180489800-180494400	Weak transcription	HUVEC	blood vessel
8	chr1:180490800-180493800	Weak transcription	Lung	lung
9	chr1:180491000-180499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:180491400-180493400	Weak transcription	Right Ventricle	heart
11	chr1:180491400-180493800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:180491400-180494000	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:180491400-180496200	Weak transcription	A549	lung
14	chr1:180491400-180496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:180491400-180499400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
17	chr1:180492000-180494000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:180492000-180494000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:180492000-180494800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:180492000-180495400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:180492000-180495400	Weak transcription	K562	blood
22	chr1:180492200-180493400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:180492200-180494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:180492200-180494000	Weak transcription	Fetal Heart	heart
25	chr1:180492200-180494600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:180492200-180494800	Weak transcription	Fetal Intestine Large	intestine
27	chr1:180492200-180495800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:180492400-180493400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:180492400-180493800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:180492400-180496400	Weak transcription	NHEK	skin
31	chr1:180492400-180499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:180492400-180503000	Weak transcription	Pancreas	Pancrea
33	chr1:180492600-180493400	Weak transcription	Left Ventricle	heart
34	chr1:180492600-180493800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:180492600-180495400	Weak transcription	HepG2	liver
36	chr1:180492600-180498000	Weak transcription	HSMMtube	muscle
37	chr1:180493000-180496200	Weak transcription	Hela-S3	cervix
38	chr1:180493200-180493400	Enhancers	Right Atrium	heart
39	chr1:180493200-180494600	Enhancers	HMEC	breast
40	chr1:180493200-180495000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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