Variant report

Variant	rs17697397
Chromosome Location	chr6:11493562-11493563
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11230707..11237186-chr6:11493072..11498269,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10456073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10456408	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10456409	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947294	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947297	0.83[ASN][1000 genomes]
rs10947298	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947299	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947300	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947301	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947305	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947330	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10947400	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947402	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947403	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12189605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189776	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12189829	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12190208	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12191269	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12191798	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12192607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12192728	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12193222	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12193579	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12194303	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12194423	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12194504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12194522	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12194708	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12195075	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195374	0.86[EUR][1000 genomes]
rs12196157	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12197783	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12199315	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12199737	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12201467	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201652	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12202370	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12203104	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12203396	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12203843	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12204093	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12207526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12207574	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208383	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208387	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209347	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209878	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12209963	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12210023	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210076	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211376	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12211930	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12212790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12214484	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12215719	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12524640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12525082	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526369	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12529805	1.00[YRI][hapmap]
rs16868542	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16868544	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16871460	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16871461	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16871481	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16871482	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16871484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17697296	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17697372	0.98[ASN][1000 genomes]
rs17764876	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17764967	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275398	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28651839	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs489364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132761	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs566535	0.81[ASN][1000 genomes]
rs566568	0.81[ASN][1000 genomes]
rs673633	0.81[ASN][1000 genomes]
rs6907207	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs821543	0.81[ASN][1000 genomes]
rs9461842	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461895	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469217	0.91[JPT][hapmap]
rs9469363	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9469368	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9469544	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469545	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469546	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469548	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469550	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469561	0.86[EUR][1000 genomes]
rs9469563	0.86[EUR][1000 genomes]
rs9791196	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3357042	chr6:11489266-11493964	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3396914	chr6:11489566-11493564	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3441435	chr6:11489666-11493664	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11483800-11495000	Weak transcription	Pancreas	Pancrea
2	chr6:11486800-11496000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:11486800-11496800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:11487000-11495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:11487400-11495800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:11487400-11495800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:11491800-11495800	Weak transcription	Fetal Kidney	kidney
8	chr6:11491800-11497200	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:11492000-11493600	Enhancers	NHDF-Ad	bronchial
10	chr6:11492000-11496200	Enhancers	Primary B cells from cord blood	blood
11	chr6:11492000-11498200	Enhancers	A549	lung
12	chr6:11492200-11493600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:11492200-11493600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:11492200-11493800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:11492200-11497400	Enhancers	HepG2	liver
16	chr6:11492400-11493800	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:11492800-11493600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:11492800-11493600	Enhancers	Placenta	Placenta
19	chr6:11492800-11496000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:11493000-11494600	Weak transcription	Lung	lung
21	chr6:11493000-11495000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:11493000-11499800	Weak transcription	NH-A	brain
23	chr6:11493200-11494200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:11493200-11496000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:11493400-11493600	Enhancers	Fetal Stomach	stomach
26	chr6:11493400-11494800	Weak transcription	Spleen	Spleen
27	chr6:11493400-11495000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:11493400-11495000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:11493400-11496200	Weak transcription	Osteobl	bone
30	chr6:11493400-11497600	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:11493400-11498200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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