Variant report

Variant	rs17455422
Chromosome Location	chr11:57534799-57534800
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	chr11:57533309..57536452-chr11:57541142..57544188,3	K562	blood:
2	chr11:57528231..57532221-chr11:57532591..57536527,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198561	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10750870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10792110	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896644	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896653	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229109	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229119	0.85[AMR][1000 genomes]
rs11570176	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11570181	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12270209	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274865	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12363024	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12801694	0.84[ASW][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12805343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424753	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1613592	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs1624389	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1631684	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1647394	0.81[ASN][1000 genomes]
rs1647403	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs17455626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783818	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783824	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783826	1.00[JPT][hapmap]
rs1783827	1.00[JPT][hapmap]
rs1783828	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1783976	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783977	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783978	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783979	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783980	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783981	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783983	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs1783985	0.84[ASN][1000 genomes]
rs1785498	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1785499	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1786438	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1798172	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs1798173	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs1798177	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2156638	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2911728	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2956981	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2956982	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3017889	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36036499	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4611222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs471398	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs547118	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56392705	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs585337	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585761	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs588612	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs592785	0.81[ASN][1000 genomes]
rs593239	0.82[ASN][1000 genomes]
rs606499	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs615133	0.85[ASW][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[YRI][hapmap]
rs623541	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs627145	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs633129	0.85[ASW][hapmap];0.82[MEX][hapmap];0.84[YRI][hapmap]
rs639158	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs644219	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs645145	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs652191	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs652908	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs653889	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];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs658936	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs659165	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs665058	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]
rs666021	0.86[JPT][hapmap]
rs671508	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs682258	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs686489	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105506	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7115528	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7117020	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120868	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];0.90[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7479922	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947357	1.00[JPT][hapmap]
rs7948571	0.91[ASN][1000 genomes]
rs929934	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv327	chr11:57532641-57550746	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17455422	MS4A7	cis	parietal	SCAN
rs17455422	YPEL4	cis	lung	GTEx
rs17455422	TIMM10	cis	parietal	SCAN
rs17455422	ZDHHC5	Cis_1M	lymphoblastoid	RTeQTL
rs17455422	SLC43A3	cis	cerebellum	SCAN
rs17455422	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57530400-57545800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr11:57531400-57543200	Weak transcription	Primary B cells from cord blood	blood
3	chr11:57531800-57538200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:57531800-57539800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:57531800-57543200	Weak transcription	Thymus	Thymus
6	chr11:57532200-57535200	Enhancers	Brain Substantia Nigra	brain
7	chr11:57532400-57535200	Active TSS	GM12878-XiMat	blood
8	chr11:57532600-57538200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr11:57532800-57535000	Enhancers	Brain Anterior Caudate	brain
10	chr11:57532800-57535200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:57532800-57535200	Enhancers	Brain Hippocampus Middle	brain
12	chr11:57532800-57539800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:57532800-57539800	Weak transcription	NHDF-Ad	bronchial
14	chr11:57532800-57541800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:57532800-57543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:57533000-57535200	Enhancers	Liver	Liver
17	chr11:57533000-57535400	Enhancers	Small Intestine	intestine
18	chr11:57533000-57536800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:57533000-57538000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr11:57533000-57539600	Weak transcription	HMEC	breast
21	chr11:57533000-57539800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:57533000-57539800	Weak transcription	NH-A	brain
23	chr11:57533200-57534800	Weak transcription	HSMM	muscle
24	chr11:57533200-57535000	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:57533200-57535200	Enhancers	Brain Cingulate Gyrus	brain
26	chr11:57533200-57535200	Genic enhancers	Fetal Intestine Small	intestine
27	chr11:57533200-57537400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:57533200-57538000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:57533200-57539800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:57533200-57539800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:57533200-57539800	Weak transcription	HSMMtube	muscle
32	chr11:57533200-57541600	Weak transcription	Hela-S3	cervix
33	chr11:57533400-57534800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:57533400-57534800	Enhancers	Fetal Intestine Large	intestine
35	chr11:57533400-57534800	Weak transcription	Stomach Mucosa	stomach
36	chr11:57533400-57537800	Weak transcription	Fetal Thymus	thymus
37	chr11:57533400-57540200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:57533400-57540200	Weak transcription	Spleen	Spleen
39	chr11:57533400-57543000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr11:57533600-57534800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:57533600-57536600	Weak transcription	Left Ventricle	heart
42	chr11:57533600-57536600	Weak transcription	Lung	lung
43	chr11:57533600-57538000	Weak transcription	Pancreas	Pancrea
44	chr11:57533600-57538200	Weak transcription	Primary T cells from cord blood	blood
45	chr11:57533600-57538400	Weak transcription	Aorta	Aorta
46	chr11:57533600-57538400	Enhancers	HepG2	liver
47	chr11:57533600-57539600	Weak transcription	Placenta	Placenta
48	chr11:57533600-57540800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr11:57533600-57541200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:57533600-57541800	Weak transcription	Colonic Mucosa	Colon

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