Variant report

Variant	rs6969052
Chromosome Location	chr7:3902305-3902306
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	chr7:3895859..3898107-chr7:3900891..3903068,3	MCF-7	breast:

Extended variants
information (count: 183 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:174)

rs_ID	r²[population]
rs10085400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10085568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1013880	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10215004	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10215340	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10228397	0.86[ASN][1000 genomes]
rs10241703	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10242459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10243770	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10244636	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10245389	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10246449	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10250659	1.00[JPT][hapmap]
rs10252169	0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs10254099	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10256741	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10262942	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10263496	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10267786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10273444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10479833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10479834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10480105	0.89[ASN][1000 genomes]
rs10485864	0.86[ASN][1000 genomes]
rs10951315	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10951322	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10951336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10951374	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11514766	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11973090	0.88[ASN][1000 genomes]
rs11974190	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11976915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11977993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11980947	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11982345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11983563	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12112335	1.00[CHB][hapmap]
rs12531046	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12531980	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12531984	0.82[JPT][hapmap]
rs12532040	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12532171	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12532903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12532912	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12533946	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12536445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12536663	0.86[ASN][1000 genomes]
rs12537696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12538997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12539695	0.82[JPT][hapmap]
rs12540101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12540220	0.81[ASN][1000 genomes]
rs12690803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12690804	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12701219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12701221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12701227	0.87[ASN][1000 genomes]
rs12701229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12701262	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13221624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13236653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13236719	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs13245096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1476644	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1548612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1548613	0.82[JPT][hapmap]
rs1548614	0.82[JPT][hapmap]
rs17133859	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs17259867	0.82[JPT][hapmap]
rs17259924	0.82[JPT][hapmap]
rs17261199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17325709	0.82[JPT][hapmap]
rs1962783	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1962784	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1962785	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2007554	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2057919	0.88[ASN][1000 genomes]
rs2057920	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2057921	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2079376	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2079377	0.88[ASN][1000 genomes]
rs2079378	0.85[ASN][1000 genomes]
rs2097899	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2097900	0.89[ASN][1000 genomes]
rs2341959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28491320	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2880159	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2880204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28845270	0.88[ASN][1000 genomes]
rs34614163	0.89[ASN][1000 genomes]
rs34730154	0.86[ASN][1000 genomes]
rs34960833	0.89[ASN][1000 genomes]
rs35261333	0.89[ASN][1000 genomes]
rs35712888	0.88[ASN][1000 genomes]
rs41873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4431501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6462361	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs6462401	0.82[CEU][hapmap]
rs6462407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6462411	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6462412	0.88[ASN][1000 genomes]
rs6462413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6462423	0.86[ASN][1000 genomes]
rs6462447	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs6943646	0.82[JPT][hapmap]
rs6944393	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6944479	0.83[ASN][1000 genomes]
rs6945778	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6948552	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6952864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6953036	0.89[ASN][1000 genomes]
rs6953282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6953604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6954370	0.88[ASN][1000 genomes]
rs6955650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6956479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6957166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6957676	0.98[ASN][1000 genomes]
rs6958385	0.88[ASN][1000 genomes]
rs6958535	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6959492	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6959674	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6959835	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6961230	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6961561	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6962058	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6962389	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6963058	0.88[ASN][1000 genomes]
rs6963674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6966030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6968148	0.88[ASN][1000 genomes]
rs6968267	0.88[ASN][1000 genomes]
rs6968272	0.88[ASN][1000 genomes]
rs6968444	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6968948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6969235	0.81[ASN][1000 genomes]
rs6970116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6971639	0.88[ASN][1000 genomes]
rs6971803	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6971828	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6971873	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6971953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6972806	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6973944	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs6975313	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs6975723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6977305	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6977844	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6978060	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6978318	0.88[ASN][1000 genomes]
rs6978964	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs6979937	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs6980085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs768721	0.82[JPT][hapmap]
rs7778705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7783415	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7786556	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7788747	0.80[ASN][1000 genomes]
rs7791274	0.82[JPT][hapmap]
rs7794504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7800775	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7804166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7806494	0.86[ASN][1000 genomes]
rs7807003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7809616	0.82[ASN][1000 genomes]
rs7811839	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs917168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs917198	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9655007	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9655343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9655347	0.86[ASN][1000 genomes]
rs9655348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs985186	0.86[ASN][1000 genomes]
rs9986911	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1027624	chr7:3808366-3923408	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv538684	chr7:3808366-3923408	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv887336	chr7:3870810-3934909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv887337	chr7:3886254-3934909	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1019190	chr7:3896634-3943566	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3900200-3902600	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr7:3900600-3902400	Enhancers	Colon Smooth Muscle	Colon
3	chr7:3900600-3902800	Enhancers	H9 Cell Line	embryonic stem cell
4	chr7:3900600-3902800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr7:3901000-3902400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:3901000-3902400	Enhancers	Adipose Nuclei	Adipose
7	chr7:3901000-3902600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr7:3901000-3902800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr7:3901000-3902800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr7:3901200-3902400	Weak transcription	Lung	lung
11	chr7:3901200-3902600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:3901200-3902600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr7:3901200-3902800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr7:3901200-3902800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr7:3901200-3959600	Weak transcription	Pancreas	Pancrea
16	chr7:3902000-3907000	Weak transcription	Fetal Stomach	stomach
17	chr7:3902200-3902600	Enhancers	Fetal Lung	lung
18	chr7:3902200-3902800	Enhancers	Stomach Smooth Muscle	stomach
19	chr7:3902200-3907400	Weak transcription	Muscle Satellite Cultured Cells	--

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