Variant report

Variant	rs512780
Chromosome Location	chr11:74545378-74545379
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	chr11:74542471..74545702-chr11:74546524..74550325,4	K562	blood:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11236269	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11605604	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs12363224	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1282460	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1282690	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1282692	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap]
rs1282695	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1292895	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs1297319	0.84[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs1303525	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1583342	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2033532	0.86[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2919057	0.93[JPT][hapmap]
rs41531051	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4245439	0.82[JPT][hapmap]
rs471462	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs473080	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs473256	0.86[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs480840	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs483615	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944945	0.83[LWK][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap]
rs497772	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs502225	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs505688	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs508319	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs511890	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap]
rs513137	0.92[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs519741	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs527529	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs529249	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs529488	0.86[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs537054	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap]
rs538502	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543244	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs546643	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs550491	0.88[CHB][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs550980	0.81[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap]
rs557483	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs561589	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs565767	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs567956	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs568558	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs568758	0.81[CEU][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs571446	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs577102	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs580142	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs590105	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs599722	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap]
rs603062	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs614832	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs624786	0.81[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap]
rs625268	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs641584	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap]
rs643807	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs646287	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs688665	0.82[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs9444	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]
rs997465	0.93[ASW][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs512780	RNF169	cis	multi-tissue	Pritchard
rs512780	PLEKHB1	cis	cerebellum	SCAN
rs512780	XRRA1	cis	Whole Blood	GTEx
rs512780	XRRA1	cis	multi-tissue	Pritchard
rs512780	KRTAP5-10	cis	parietal	SCAN
rs512780	XRRA1	cis	parietal	SCAN
rs512780	RNF169	cis	cerebellum	SCAN
rs512780	XRRA1	cis	lymphoblastoid	seeQTL
rs512780	XRRA1	cis	Muscle Skeletal	GTEx
rs512780	FCHSD2	cis	cerebellum	SCAN
rs512780	RNF169	cis	lymphoblastoid	seeQTL
rs512780	XRRA1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74502800-74545600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
3	chr11:74533400-74545800	Weak transcription	Left Ventricle	heart
4	chr11:74533600-74546200	Weak transcription	Aorta	Aorta
5	chr11:74533600-74546200	Weak transcription	Psoas Muscle	Psoas
6	chr11:74533600-74546400	Weak transcription	Right Ventricle	heart
7	chr11:74533800-74553200	Weak transcription	Fetal Heart	heart
8	chr11:74536000-74546400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:74538200-74545800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:74538200-74545800	Weak transcription	Brain Angular Gyrus	brain
11	chr11:74538200-74546400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:74538400-74545400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:74538400-74545400	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:74538400-74545600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:74538400-74545600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:74538400-74545600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:74538400-74545600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:74538400-74545600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:74538400-74545600	Weak transcription	Gastric	stomach
20	chr11:74538400-74545600	Weak transcription	Lung	lung
21	chr11:74538400-74545600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr11:74538400-74545800	Weak transcription	Colonic Mucosa	Colon
23	chr11:74538400-74545800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr11:74538400-74545800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:74538400-74545800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:74538400-74545800	Weak transcription	HMEC	breast
27	chr11:74538400-74545800	Weak transcription	HUVEC	blood vessel
28	chr11:74538400-74546000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:74538400-74546000	Weak transcription	Brain Substantia Nigra	brain
30	chr11:74538400-74546000	Weak transcription	Pancreas	Pancrea
31	chr11:74538400-74546200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr11:74538400-74546200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:74538400-74546400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr11:74538400-74546400	Weak transcription	Esophagus	oesophagus
35	chr11:74538400-74546400	Weak transcription	HSMMtube	muscle
36	chr11:74538400-74546400	Weak transcription	K562	blood
37	chr11:74538400-74546600	Weak transcription	NHLF	lung
38	chr11:74538400-74553200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:74538400-74559000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:74538400-74560000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr11:74538600-74545600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:74538600-74545600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:74538600-74545600	Weak transcription	Thymus	Thymus
44	chr11:74538600-74545600	Weak transcription	Spleen	Spleen
45	chr11:74538600-74545800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr11:74538600-74545800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:74538600-74545800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:74538600-74545800	Weak transcription	Brain Anterior Caudate	brain
49	chr11:74538600-74545800	Weak transcription	Brain Germinal Matrix	brain
50	chr11:74538600-74545800	Weak transcription	Fetal Stomach	stomach

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