Variant report

Variant	rs11968704
Chromosome Location	chr6:39463661-39463662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39463170..39464911-chr6:39479174..39481419,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10947813	0.81[ASN][1000 genomes]
rs11961693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11962587	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11964924	0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11968279	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11969059	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11969395	0.86[ASN][1000 genomes]
rs12175102	0.81[EUR][1000 genomes]
rs12664369	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1546910	0.81[CHB][hapmap]
rs16892158	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs1927774	0.86[JPT][hapmap]
rs1927775	0.86[JPT][hapmap]
rs1952362	0.86[JPT][hapmap]
rs2038198	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2073134	0.80[CHB][hapmap]
rs2235817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28533484	0.84[ASN][1000 genomes]
rs3736735	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4482968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4482969	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4540261	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs4605875	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711598	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs4714253	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs4714255	0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4714256	0.83[CHB][hapmap]
rs56951565	0.88[ASN][1000 genomes]
rs57703896	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57799480	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59617761	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59724542	0.94[ASN][1000 genomes]
rs6901155	0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs73732127	0.81[ASN][1000 genomes]
rs9296299	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9296300	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs9349120	0.83[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9357307	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs9357308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357311	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9367008	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs9367009	0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9367012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367015	0.85[ASN][1000 genomes]
rs9367016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369119	0.89[CHB][hapmap]
rs9369123	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369124	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9369126	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs9380861	0.81[ASN][1000 genomes]
rs9380863	0.86[JPT][hapmap]
rs9380864	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380865	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9380867	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9380868	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs9380871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380872	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380876	0.81[ASN][1000 genomes]
rs9380877	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380879	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9380880	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394592	0.83[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9394594	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs9394595	0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9394598	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs9394599	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs9394600	0.89[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs9394601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9394607	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394608	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9394609	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9394611	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394614	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394615	0.81[EUR][1000 genomes]
rs9462553	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs9471113	0.84[CHB][hapmap]
rs9471118	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv885823	chr6:39421715-39526867	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39455400-39465200	Weak transcription	Right Atrium	heart
2	chr6:39456800-39468400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:39461600-39464200	Weak transcription	Adipose Nuclei	Adipose
4	chr6:39461600-39464600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:39461600-39464800	Weak transcription	NHDF-Ad	bronchial
6	chr6:39461800-39464800	Weak transcription	Placenta	Placenta
7	chr6:39461800-39465200	Weak transcription	Fetal Kidney	kidney
8	chr6:39462000-39464400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:39462000-39465000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:39462200-39463800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:39462600-39464200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:39462600-39464400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:39462600-39464400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:39462600-39464400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:39462600-39466200	Enhancers	Fetal Lung	lung
16	chr6:39462800-39464200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr6:39462800-39464200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:39462800-39464400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:39462800-39464400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:39462800-39465000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:39462800-39465000	Enhancers	H9 Cell Line	embryonic stem cell
22	chr6:39462800-39467000	Enhancers	Fetal Stomach	stomach
23	chr6:39463000-39466400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:39463200-39464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:39463200-39464400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:39463400-39463800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr6:39463600-39463800	Enhancers	Fetal Muscle Leg	muscle
28	chr6:39463600-39464000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr6:39463600-39464000	Enhancers	Stomach Smooth Muscle	stomach

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