Variant report

Variant	rs868860
Chromosome Location	chr11:9758896-9758897
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	chr11:9756797..9759771-chr11:9761675..9763540,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1045634	0.85[JPT][hapmap]
rs1056593	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1056674	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770061	0.85[JPT][hapmap]
rs10840300	0.80[JPT][hapmap]
rs11042498	0.85[JPT][hapmap]
rs11821544	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11821692	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11825952	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11828354	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16906967	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16907071	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs1845884	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28607967	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3197265	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34696762	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751001	1.00[CEU][hapmap]
rs3763862	0.85[JPT][hapmap]
rs3817010	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829252	0.85[JPT][hapmap]
rs4910500	0.85[JPT][hapmap]
rs55959510	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56029305	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56096143	0.82[ASN][1000 genomes]
rs56294870	0.81[ASN][1000 genomes]
rs56340721	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57070018	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57590863	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57650149	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57843161	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57864531	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58073079	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58217715	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58765157	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59070186	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60195226	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60544361	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60548107	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60601382	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60929104	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61059316	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61284089	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61469272	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6483649	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483650	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483651	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483654	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6483655	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6483657	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6483658	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7113055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7114514	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7928407	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7935267	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936721	0.85[JPT][hapmap]
rs7939896	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7940708	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7940826	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7946920	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949343	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950075	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868861	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868862	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS 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 miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9733600-9761600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9733800-9759800	Weak transcription	Fetal Heart	heart
3	chr11:9740000-9762000	Weak transcription	Brain Angular Gyrus	brain
4	chr11:9742200-9759800	Weak transcription	Fetal Kidney	kidney
5	chr11:9742200-9779400	Weak transcription	Fetal Brain Male	brain
6	chr11:9744600-9761400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:9745000-9775600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:9749000-9761800	Weak transcription	Small Intestine	intestine
9	chr11:9749000-9764400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:9749000-9764400	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr11:9749400-9764400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:9749600-9764400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:9751000-9764400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:9753800-9764400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:9754000-9764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:9754200-9764400	Strong transcription	Adipose Nuclei	Adipose
17	chr11:9754400-9761600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:9754400-9764400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr11:9754800-9764400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:9755000-9759600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:9755000-9759800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:9755000-9761200	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:9755000-9761400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr11:9755000-9761600	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:9755000-9761800	Weak transcription	Right Ventricle	heart
26	chr11:9755000-9777600	Weak transcription	Colonic Mucosa	Colon
27	chr11:9755200-9759800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:9755400-9759800	Weak transcription	Gastric	stomach
29	chr11:9755400-9760800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:9755400-9761600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:9755400-9769800	Weak transcription	Pancreas	Pancrea
32	chr11:9756000-9759000	ZNF genes & repeats	GM12878-XiMat	blood
33	chr11:9756200-9759600	Weak transcription	NHLF	lung
34	chr11:9756600-9759800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:9756600-9762800	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr11:9756600-9764400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:9756800-9762400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:9756800-9764400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr11:9756800-9764400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:9757000-9759000	Genic enhancers	NHEK	skin
41	chr11:9757000-9762600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:9757200-9759600	Weak transcription	Fetal Lung	lung
43	chr11:9757200-9760200	Genic enhancers	HUVEC	blood vessel
44	chr11:9757200-9760600	Genic enhancers	Placenta	Placenta
45	chr11:9757400-9759400	Weak transcription	HMEC	breast
46	chr11:9757400-9759600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:9757400-9759600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr11:9757400-9760400	Genic enhancers	Primary B cells from cord blood	blood
49	chr11:9757400-9760600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr11:9757400-9761400	Weak transcription	NH-A	brain

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