Variant report

Variant	rs9399652
Chromosome Location	chr6:101120006-101120007
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	chr6:101115915..101118042-chr6:101119236..101121242,2	MCF-7	breast:

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1006398	0.80[EUR][1000 genomes]
rs1039031	0.98[ASN][1000 genomes]
rs1039032	0.98[ASN][1000 genomes]
rs1039033	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10872622	0.98[ASN][1000 genomes]
rs10872623	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10872628	0.81[ASN][1000 genomes]
rs11155596	0.83[ASN][1000 genomes]
rs11155606	0.81[ASN][1000 genomes]
rs11155610	0.81[ASN][1000 genomes]
rs11756783	0.96[EUR][1000 genomes]
rs12189562	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12190574	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12193960	0.82[ASN][1000 genomes]
rs12199888	0.83[ASN][1000 genomes]
rs12201852	0.82[ASN][1000 genomes]
rs12207086	0.82[ASN][1000 genomes]
rs12209887	1.00[ASN][1000 genomes]
rs12210312	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12212736	0.82[ASN][1000 genomes]
rs12214151	0.81[ASN][1000 genomes]
rs12215909	0.94[ASN][1000 genomes]
rs12216199	0.82[ASN][1000 genomes]
rs12216304	0.81[ASN][1000 genomes]
rs12525128	0.91[EUR][1000 genomes]
rs12526352	0.96[EUR][1000 genomes]
rs12660725	0.85[JPT][hapmap]
rs13201267	0.89[EUR][1000 genomes]
rs13208757	0.95[ASN][1000 genomes]
rs151572	0.81[ASN][1000 genomes]
rs151637	0.81[ASN][1000 genomes]
rs151640	0.98[ASN][1000 genomes]
rs17190683	0.93[EUR][1000 genomes]
rs17794439	0.85[EUR][1000 genomes]
rs180963	0.80[EUR][1000 genomes]
rs2036052	0.83[ASN][1000 genomes]
rs2134044	0.94[EUR][1000 genomes]
rs239189	0.81[ASN][1000 genomes]
rs239190	0.83[ASN][1000 genomes]
rs239193	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs239194	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs239195	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs239196	0.97[EUR][1000 genomes]
rs239197	0.83[ASN][1000 genomes]
rs239198	1.00[EUR][1000 genomes]
rs239199	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs239201	0.83[ASN][1000 genomes]
rs239203	0.83[ASN][1000 genomes]
rs239204	0.83[ASN][1000 genomes]
rs239206	0.83[ASN][1000 genomes]
rs239207	0.83[ASN][1000 genomes]
rs239211	0.83[ASN][1000 genomes]
rs239212	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs239216	0.82[ASN][1000 genomes]
rs239217	0.82[ASN][1000 genomes]
rs239219	0.83[ASN][1000 genomes]
rs239221	0.81[ASN][1000 genomes]
rs239222	0.81[ASN][1000 genomes]
rs239226	0.81[ASN][1000 genomes]
rs239227	0.81[ASN][1000 genomes]
rs239229	0.81[ASN][1000 genomes]
rs239230	0.81[ASN][1000 genomes]
rs239231	0.81[ASN][1000 genomes]
rs239232	0.81[ASN][1000 genomes]
rs239234	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs239235	0.81[ASN][1000 genomes]
rs239236	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239237	0.81[ASN][1000 genomes]
rs239238	0.81[ASN][1000 genomes]
rs240111	0.93[ASN][1000 genomes]
rs240149	0.97[ASN][1000 genomes]
rs240151	0.97[ASN][1000 genomes]
rs240152	0.97[ASN][1000 genomes]
rs369125	0.82[ASN][1000 genomes]
rs370757	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3818233	0.95[EUR][1000 genomes]
rs41288423	0.98[ASN][1000 genomes]
rs4329121	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4461738	0.82[GIH][hapmap];0.85[JPT][hapmap]
rs454747	0.84[ASN][1000 genomes]
rs58266877	0.81[ASN][1000 genomes]
rs6570922	0.81[ASN][1000 genomes]
rs6903665	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6904959	1.00[ASN][1000 genomes]
rs6905221	0.82[ASN][1000 genomes]
rs6907240	0.83[ASN][1000 genomes]
rs6907444	0.98[ASN][1000 genomes]
rs6916468	0.99[ASN][1000 genomes]
rs6928418	0.91[EUR][1000 genomes]
rs6937520	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6938440	0.82[ASN][1000 genomes]
rs7356804	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7452753	0.85[EUR][1000 genomes]
rs7740826	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7759463	0.83[EUR][1000 genomes]
rs7766621	0.87[YRI][hapmap]
rs9373571	0.96[EUR][1000 genomes]
rs9373574	0.94[EUR][1000 genomes]
rs9377193	0.84[EUR][1000 genomes]
rs9386233	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9390502	0.91[EUR][1000 genomes]
rs9390626	0.94[EUR][1000 genomes]
rs9399641	0.96[EUR][1000 genomes]
rs9399656	0.96[EUR][1000 genomes]
rs9403962	0.93[EUR][1000 genomes]
rs9403997	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028016	chr6:101001055-101158822	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv886445	chr6:101004751-101240763	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886448	chr6:101018032-101123503	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv886449	chr6:101018032-101147095	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv886450	chr6:101018032-101168137	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv886451	chr6:101018032-101172328	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv886452	chr6:101018032-101192051	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv886453	chr6:101018032-101203051	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv463988	chr6:101036713-101158950	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv604266	chr6:101036713-101158950	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv886454	chr6:101049108-101123503	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv886455	chr6:101049108-101203051	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv886456	chr6:101049108-101277926	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv463990	chr6:101058886-101123503	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv604269	chr6:101058886-101123503	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv604270	chr6:101058886-101196080	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv604271	chr6:101072307-101158950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv463991	chr6:101072307-101196080	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv604272	chr6:101072307-101196080	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv463992	chr6:101072307-101197953	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
22	nsv604273	chr6:101072307-101197953	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
23	nsv604274	chr6:101078718-101196080	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	nsv1027288	chr6:101091434-101121237	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv1032826	chr6:101091434-101147095	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv1028583	chr6:101091434-101152631	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv1015465	chr6:101091434-101157493	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv1031817	chr6:101091995-101157493	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9399652	ASCC3	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101071600-101127800	Weak transcription	Hela-S3	cervix
2	chr6:101093000-101145800	Weak transcription	Fetal Thymus	thymus
3	chr6:101100400-101131400	Weak transcription	Liver	Liver
4	chr6:101100600-101149800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:101100800-101122400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:101100800-101124400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:101100800-101126600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:101100800-101129200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:101100800-101147600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:101100800-101164600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:101101400-101120800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:101103800-101121400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:101103800-101126600	Weak transcription	Placenta	Placenta
14	chr6:101103800-101129400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:101103800-101129600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:101103800-101143600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:101104000-101135000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:101110000-101147600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:101110400-101146800	Weak transcription	Primary T cells from cord blood	blood
20	chr6:101110800-101129800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:101111200-101168200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:101111600-101120800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:101111600-101121200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:101111600-101130200	Weak transcription	HUVEC	blood vessel
25	chr6:101111600-101168000	Weak transcription	NHDF-Ad	bronchial
26	chr6:101111800-101121400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:101111800-101131200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:101111800-101139800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:101111800-101147200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:101111800-101147200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:101111800-101168200	Weak transcription	Osteobl	bone
32	chr6:101112000-101161200	Weak transcription	HMEC	breast
33	chr6:101112800-101121200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:101113400-101121400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:101118200-101123200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:101118600-101134000	Weak transcription	Psoas Muscle	Psoas
37	chr6:101118600-101168000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:101118800-101147400	Weak transcription	GM12878-XiMat	blood
39	chr6:101119000-101126800	Weak transcription	HSMM	muscle
40	chr6:101119000-101147000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:101119200-101165600	Weak transcription	NH-A	brain
42	chr6:101119400-101120200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:101119400-101181200	Weak transcription	Left Ventricle	heart
44	chr6:101119600-101120800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:101119800-101121200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr6:101119800-101121400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:101119800-101124200	Weak transcription	Dnd41	blood
48	chr6:101119800-101133400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:101119800-101146800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:101119800-101146800	Weak transcription	Primary B cells from cord blood	blood

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