Variant report

Variant	rs9444
Chromosome Location	chr11:74553074-74553075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:74552211-74556846	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:74552536..74554674-chr11:74560171..74562245,2	K562	blood:
2	chr11:74550798..74553553-chr11:74554025..74555880,2	MCF-7	breast:
3	chr11:74551532..74554189-chr11:74554328..74556316,4	K562	blood:
4	chr11:74551815..74554454-chr11:74557454..74559608,2	K562	blood:
5	chr11:74449856..74451588-chr11:74552706..74555219,2	K562	blood:
6	chr11:74551525..74553766-chr11:74563114..74564936,2	K562	blood:

No data

Variant related genes	Relation type
RN7SL239P	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11236269	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11605604	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12363224	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1282460	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282461	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1282689	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1282690	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1282692	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1282695	0.82[AMR][1000 genomes]
rs1292895	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1297319	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1303525	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1315297	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1583342	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028343	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2028344	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2033532	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2919057	0.94[JPT][hapmap]
rs41531051	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4245439	0.84[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs471462	0.92[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs473080	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs473256	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs480840	0.92[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs483615	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4944945	0.87[LWK][hapmap];0.92[YRI][hapmap]
rs495246	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs497772	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs502225	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs505688	0.92[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs508319	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs511021	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs511890	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs512780	0.92[ASW][hapmap];0.85[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs513137	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs519741	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs527529	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs529249	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs529488	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs537054	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs538502	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs543244	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs546643	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs550491	0.87[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs550869	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs550980	0.85[CEU][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs557483	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs561589	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs562265	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs565767	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs567956	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs568558	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs568758	0.96[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs571446	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573925	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs577063	0.86[EUR][1000 genomes]
rs577102	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs580142	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs590105	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs599722	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs603062	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs614832	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs616085	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs624786	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs625268	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs629573	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs643807	0.92[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs646287	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs688665	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997465	0.85[ASW][hapmap];0.87[JPT][hapmap];0.85[MKK][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	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
4	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9444	RNF169	cis	multi-tissue	Pritchard
rs9444	XRRA1	cis	Adipose Subcutaneous	GTEx
rs9444	XRRA1	cis	Esophagus Mucosa	GTEx
rs9444	XRRA1	cis	Thyroid	GTEx
rs9444	XRRA1	cis	Whole Blood	GTEx
rs9444	RP11-147I3.1	cis	Thyroid	GTEx
rs9444	XRRA1	cis	Muscle Skeletal	GTEx
rs9444	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs9444	XRRA1	cis	lung	GTEx
rs9444	XRRA1	cis	Artery Tibial	GTEx
rs9444	XRRA1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
2	chr11:74533800-74553200	Weak transcription	Fetal Heart	heart
3	chr11:74538400-74553200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:74538400-74559000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:74538400-74560000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:74538600-74554600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:74539200-74557200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:74541800-74556400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:74543800-74565800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:74544000-74557400	Strong transcription	Dnd41	blood
11	chr11:74544000-74557600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:74544200-74557200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:74544200-74558400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr11:74545200-74556800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr11:74545600-74564600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr11:74545600-74568400	Strong transcription	Fetal Intestine Large	intestine
18	chr11:74545800-74559800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:74545800-74560400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:74545800-74565000	Strong transcription	Fetal Muscle Leg	muscle
21	chr11:74546000-74566800	Strong transcription	Fetal Stomach	stomach
22	chr11:74546200-74559400	Strong transcription	Fetal Lung	lung
23	chr11:74547400-74556000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr11:74547600-74557600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:74547600-74571400	Weak transcription	Fetal Brain Male	brain
26	chr11:74547800-74555200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr11:74547800-74562800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr11:74548000-74553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:74548000-74553200	Weak transcription	Spleen	Spleen
30	chr11:74548000-74555400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:74548000-74558200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr11:74548000-74560600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:74548400-74554000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:74548600-74555400	Weak transcription	Small Intestine	intestine
35	chr11:74548800-74560200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:74549000-74553400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr11:74549400-74567600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr11:74549600-74553200	Weak transcription	Colon Smooth Muscle	Colon
39	chr11:74549600-74553200	Weak transcription	HSMMtube	muscle
40	chr11:74549800-74553200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:74549800-74553200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr11:74549800-74553200	Weak transcription	Adipose Nuclei	Adipose
43	chr11:74549800-74553200	Weak transcription	Brain Anterior Caudate	brain
44	chr11:74549800-74553200	Weak transcription	NHLF	lung
45	chr11:74549800-74553800	Weak transcription	Pancreas	Pancrea
46	chr11:74549800-74554000	Weak transcription	Esophagus	oesophagus
47	chr11:74549800-74560400	Weak transcription	Right Atrium	heart
48	chr11:74550000-74553200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:74550000-74553600	Weak transcription	Ovary	ovary
50	chr11:74550400-74553200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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