Variant report

Variant	rs6905847
Chromosome Location	chr6:45487944-45487945
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45389741..45391905-chr6:45485507..45488244,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction
ENSG00000271857	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10214519	1.00[JPT][hapmap]
rs10485422	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948237	1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs10948238	0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11756145	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200428	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12195878	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197948	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12204049	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209785	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210100	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12215249	0.85[ASN][1000 genomes]
rs1316330	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1317777	1.00[JPT][hapmap]
rs13201287	0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207392	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13208741	0.90[ASN][1000 genomes]
rs1928533	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1934327	1.00[JPT][hapmap]
rs1934329	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2031966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[JPT][hapmap]
rs2677110	1.00[JPT][hapmap]
rs2790098	1.00[JPT][hapmap]
rs2819864	1.00[JPT][hapmap]
rs2819866	1.00[JPT][hapmap]
rs4438954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4714854	1.00[JPT][hapmap]
rs4714859	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6458445	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458446	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458447	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6904353	0.82[ASW][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6905181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915569	1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs6932037	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72864634	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748231	0.94[ASW][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs7754187	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7755257	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7756094	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7760160	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7771889	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7772562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472494	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1019561	chr6:45485826-45535222	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv538214	chr6:45485826-45535222	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6905847	KLHDC3	cis	cerebellum	SCAN
rs6905847	C6orf141	cis	cerebellum	SCAN
rs6905847	ZNF318	cis	parietal	SCAN
rs6905847	RPL7L1	cis	cerebellum	SCAN
rs6905847	RUNX2	cis	multi-tissue	Pritchard

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45465000-45521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr6:45466800-45488200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:45466800-45497200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:45474000-45489000	Weak transcription	Primary T cells from cord blood	blood
5	chr6:45479000-45500000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:45480200-45488400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:45481000-45500200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:45481400-45488200	Weak transcription	Fetal Lung	lung
9	chr6:45481400-45488600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:45481400-45500200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:45481400-45514600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:45482000-45488400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:45482000-45490800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:45482000-45500000	Weak transcription	NHDF-Ad	bronchial
15	chr6:45482200-45488600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:45482400-45494600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:45482600-45488000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:45482600-45488200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:45482600-45488200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:45482600-45489800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:45482600-45490200	Weak transcription	Dnd41	blood
22	chr6:45482600-45490400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:45482600-45490400	Weak transcription	NHLF	lung
24	chr6:45482600-45500200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:45482600-45503600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:45482800-45488000	Weak transcription	Stomach Mucosa	stomach
27	chr6:45482800-45514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:45483000-45488600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr6:45483000-45490400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:45483800-45488000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:45484000-45488000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:45484200-45488000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:45484200-45488200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:45484400-45509400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:45484400-45514600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:45485200-45488800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:45485200-45489800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:45486000-45489000	Genic enhancers	HSMM	muscle
39	chr6:45486200-45488600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:45486200-45488600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr6:45486400-45488600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:45486400-45490000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:45486400-45491800	Weak transcription	Hela-S3	cervix
44	chr6:45487000-45488200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:45487000-45490800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr6:45487200-45489400	Enhancers	Osteobl	bone
47	chr6:45487400-45488600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:45487600-45488400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:45487600-45488600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:45487600-45489000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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