Variant report

Variant	rs665058
Chromosome Location	chr11:57579166-57579167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57508369..57511140-chr11:57577565..57580322,2	MCF-7	breast:
2	chr11:57570082..57573080-chr11:57578840..57580964,2	MCF-7	breast:
3	chr11:57568699..57575383-chr11:57575572..57580605,8	K562	blood:

Variant related genes	Relation type
ENSG00000211450	Chromatin interaction
ENSG00000198561	Chromatin interaction
ENSG00000254732	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10750870	1.00[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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10792110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896653	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229109	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229119	0.86[AMR][1000 genomes]
rs11570176	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11570181	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12270209	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12274865	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12363024	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12805343	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1424753	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1613592	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1624389	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1631684	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1647403	0.86[JPT][hapmap]
rs17455422	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17455626	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1783818	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783824	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1783826	1.00[JPT][hapmap]
rs1783827	1.00[JPT][hapmap]
rs1783828	1.00[JPT][hapmap]
rs1783976	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1783977	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1783978	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1783979	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1783980	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1783981	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1783983	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1785498	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1785499	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1786438	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1798172	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1798173	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1798177	1.00[JPT][hapmap]
rs2156638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2911728	0.84[AMR][1000 genomes]
rs2956981	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2956982	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3017889	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36036499	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4611222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs471398	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs547118	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56392705	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs585337	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs585761	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs588612	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs592785	0.83[ASN][1000 genomes]
rs593239	0.84[ASN][1000 genomes]
rs606499	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs615133	0.82[MEX][hapmap]
rs623541	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627145	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs633129	0.82[MEX][hapmap]
rs639158	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644219	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645145	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652191	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652908	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs653889	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658936	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs659165	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666021	0.84[JPT][hapmap]
rs671508	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs682258	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686489	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7105506	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7115528	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7117020	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7120868	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7479922	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7947357	1.00[JPT][hapmap]
rs7948571	0.96[ASN][1000 genomes]
rs929934	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs665058	SLC43A3	cis	cerebellum	SCAN
rs665058	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs665058	TIMM10	cis	parietal	SCAN
rs665058	ZDHHC5	Cis_1M	lymphoblastoid	RTeQTL
rs665058	MS4A7	cis	parietal	SCAN
rs665058	YPEL4	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57556400-57587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57568200-57585800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr11:57568200-57586000	Strong transcription	Fetal Muscle Leg	muscle
4	chr11:57568200-57588200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:57568400-57586600	Strong transcription	Placenta	Placenta
6	chr11:57568600-57581000	Strong transcription	K562	blood
7	chr11:57568600-57585800	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:57568600-57586000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:57568600-57586000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:57568600-57586400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:57568600-57586600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:57568600-57587000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:57568600-57587200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:57568600-57589000	Strong transcription	NHLF	lung
15	chr11:57568800-57585200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr11:57568800-57585600	Strong transcription	Fetal Intestine Large	intestine
17	chr11:57568800-57589000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:57568800-57589000	Strong transcription	NH-A	brain
19	chr11:57569000-57579200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:57569000-57580600	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr11:57569000-57583800	Strong transcription	NHDF-Ad	bronchial
22	chr11:57569000-57584800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:57569000-57584800	Strong transcription	HMEC	breast
24	chr11:57569000-57585000	Strong transcription	HepG2	liver
25	chr11:57569000-57585800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr11:57569000-57586000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:57569000-57586400	Strong transcription	Brain Germinal Matrix	brain
28	chr11:57569000-57587000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:57569000-57587000	Strong transcription	NHEK	skin
30	chr11:57569000-57587200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:57569000-57587400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:57569000-57587800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:57569000-57588800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:57569000-57589200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:57569200-57579200	Strong transcription	Brain Cingulate Gyrus	brain
36	chr11:57569200-57579200	Strong transcription	Fetal Thymus	thymus
37	chr11:57569200-57579600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:57569200-57579800	Strong transcription	Brain Anterior Caudate	brain
39	chr11:57569200-57579800	Strong transcription	Small Intestine	intestine
40	chr11:57569200-57580400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:57569200-57580800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:57569200-57581200	Strong transcription	Hela-S3	cervix
43	chr11:57569200-57583200	Strong transcription	Fetal Brain Male	brain
44	chr11:57569200-57584800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:57569200-57584800	Strong transcription	A549	lung
46	chr11:57569200-57585000	Strong transcription	Ovary	ovary
47	chr11:57569200-57585200	Strong transcription	Fetal Intestine Small	intestine
48	chr11:57569200-57585400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr11:57569200-57585400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr11:57569200-57585800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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