Variant report

Variant	rs1075702
Chromosome Location	chr11:86461180-86461181
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	chr11:86318979..86319867-chr11:86460274..86461251,4	MCF-7	breast:
2	chr11:86383122..86384948-chr11:86459289..86461430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151376	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10751141	0.82[CHB][hapmap]
rs10898534	0.85[ASN][1000 genomes]
rs11234783	0.96[ASN][1000 genomes]
rs11234795	0.83[ASN][1000 genomes]
rs11234834	0.81[CHB][hapmap]
rs11601553	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12576018	0.86[ASN][1000 genomes]
rs12802848	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17211926	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs17819068	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2433406	0.91[CHB][hapmap]
rs2433407	0.87[CHB][hapmap]
rs2433408	0.91[CHB][hapmap]
rs2433409	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs2433411	0.82[ASN][1000 genomes]
rs2433424	0.82[ASN][1000 genomes]
rs2433425	0.82[ASN][1000 genomes]
rs2433426	0.83[ASN][1000 genomes]
rs2433427	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs2433428	0.85[ASN][1000 genomes]
rs2433429	0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs2433431	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs2433432	0.91[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs2433433	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2433434	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2433435	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2433436	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2433438	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2433439	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2433440	0.92[ASN][1000 genomes]
rs2433441	0.92[ASN][1000 genomes]
rs2512978	0.92[ASN][1000 genomes]
rs2512979	0.92[ASN][1000 genomes]
rs2512996	0.95[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs2512997	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs2512998	0.81[ASN][1000 genomes]
rs2512999	0.86[ASN][1000 genomes]
rs2513000	0.85[ASN][1000 genomes]
rs2513001	0.84[ASN][1000 genomes]
rs2513003	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs2513004	0.86[ASN][1000 genomes]
rs2513005	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2513006	0.82[ASN][1000 genomes]
rs2513010	0.80[ASN][1000 genomes]
rs2513011	0.81[ASN][1000 genomes]
rs2513012	0.81[ASN][1000 genomes]
rs2513018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2513019	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3096714	0.81[ASN][1000 genomes]
rs3096715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3096716	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3096717	0.90[ASN][1000 genomes]
rs3096718	0.87[ASN][1000 genomes]
rs4128368	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4245426	0.98[ASN][1000 genomes]
rs4269941	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4307743	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4570601	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4586194	0.84[ASN][1000 genomes]
rs4943957	0.96[ASN][1000 genomes]
rs4944629	0.91[ASN][1000 genomes]
rs4944630	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs61690902	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6592315	0.81[JPT][hapmap]
rs6592317	0.82[CHB][hapmap]
rs7108176	0.82[ASN][1000 genomes]
rs7108300	0.80[ASN][1000 genomes]
rs7124794	0.83[ASN][1000 genomes]
rs7126492	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs7926713	0.81[ASN][1000 genomes]
rs7926946	0.80[ASN][1000 genomes]
rs7927257	0.80[ASN][1000 genomes]
rs7927479	0.81[ASN][1000 genomes]
rs7948063	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7951582	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]

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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1049157	chr11:86409059-86504155	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv521505	chr11:86438115-86515072	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv468775	chr11:86453415-86480716	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv555705	chr11:86453415-86480716	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv2756074	chr11:86456552-86729552	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1075702	CCDC89	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86454000-86474000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:86455000-86461200	Enhancers	Osteobl	bone
3	chr11:86455000-86461600	Enhancers	NHDF-Ad	bronchial
4	chr11:86455000-86462400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:86455200-86464600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:86456200-86462400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:86456400-86461400	Enhancers	HSMM	muscle
8	chr11:86456600-86461400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:86456600-86461600	Enhancers	HSMMtube	muscle
10	chr11:86456600-86478000	Weak transcription	Aorta	Aorta
11	chr11:86456800-86461200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:86457400-86461400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:86457600-86461400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:86458000-86461200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:86458200-86461400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:86459000-86461200	Enhancers	Stomach Smooth Muscle	stomach
17	chr11:86459200-86461400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr11:86459200-86461600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:86459400-86461600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:86459600-86461400	Enhancers	Fetal Muscle Trunk	muscle
21	chr11:86459800-86461200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:86460400-86461400	Enhancers	Fetal Muscle Leg	muscle
23	chr11:86460600-86461600	Enhancers	Adipose Nuclei	Adipose
24	chr11:86460600-86461600	Enhancers	Fetal Stomach	stomach
25	chr11:86460800-86461200	Weak transcription	Ovary	ovary
26	chr11:86460800-86461400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:86460800-86466800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:86461000-86461200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:86461000-86461200	Weak transcription	Psoas Muscle	Psoas
30	chr11:86461000-86461400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:86461000-86461400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:86461000-86461400	Enhancers	Fetal Lung	lung

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