Variant report

Variant	rs519741
Chromosome Location	chr11:74669394-74669395
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74665039..74667224-chr11:74668149..74670219,3	MCF-7	breast:
2	chr11:74667515..74671064-chr11:74674801..74677690,4	K562	blood:
3	chr11:74668433..74670131-chr11:74694358..74696257,2	MCF-7	breast:
4	chr11:74665537..74669916-chr11:74669929..74673689,6	K562	blood:
5	chr11:74662428..74664987-chr11:74667630..74670235,3	K562	blood:
6	chr11:74667608..74669880-chr11:74700969..74702927,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs11236269	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11605604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12363224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1282460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1282689	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282690	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1282692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1282695	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1292895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1297319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1315297	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1583342	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2028343	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028344	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033532	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851136	0.85[ASN][1000 genomes]
rs2919057	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs41531051	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4245439	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs471462	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs473080	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs473256	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs480840	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs483615	0.83[AMR][1000 genomes]
rs4944067	0.82[MKK][hapmap]
rs495246	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs502225	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs505688	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs508319	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs511021	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512780	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]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs527529	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs529249	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs529488	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs543244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs546643	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs550869	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550980	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs557483	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs561589	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs562265	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs565767	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs567956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs568758	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571446	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs573925	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs577063	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs577102	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes]
rs580142	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs590105	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs594144	0.83[AFR][1000 genomes]
rs599722	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];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs614832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs616085	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624786	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643807	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs646287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs688665	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444	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]
rs997465	0.93[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs519741	XRRA1	cis	Thyroid	GTEx
rs519741	XRRA1	cis	Whole Blood	GTEx
rs519741	XRRA1	cis	lymphoblastoid	seeQTL
rs519741	KRTAP5-10	cis	parietal	SCAN
rs519741	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs519741	XRRA1	cis	Adipose Subcutaneous	GTEx
rs519741	RNF169	cis	cerebellum	SCAN
rs519741	RNF169	cis	lymphoblastoid	seeQTL
rs519741	XRRA1	cis	cerebellum	SCAN
rs519741	XRRA1	cis	Muscle Skeletal	GTEx
rs519741	XRRA1	cis	lung	GTEx
rs519741	XRRA1	cis	parietal	SCAN
rs519741	RP11-147I3.1	cis	Thyroid	GTEx
rs519741	XRRA1	cis	Esophagus Mucosa	GTEx
rs519741	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs519741	XRRA1	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74661200-74688600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:74661600-74686000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:74661800-74672600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr11:74661800-74675000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:74661800-74699200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:74661800-74699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:74662000-74669800	Weak transcription	Fetal Intestine Small	intestine
8	chr11:74662000-74677600	Weak transcription	HSMMtube	muscle
9	chr11:74662000-74680800	Weak transcription	Fetal Kidney	kidney
10	chr11:74662000-74682200	Weak transcription	Aorta	Aorta
11	chr11:74662000-74682800	Weak transcription	Colonic Mucosa	Colon
12	chr11:74662200-74671000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:74662200-74671600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:74662200-74672800	Weak transcription	Gastric	stomach
15	chr11:74662200-74672800	Weak transcription	Stomach Mucosa	stomach
16	chr11:74662200-74677000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:74662200-74677200	Weak transcription	Fetal Muscle Leg	muscle
18	chr11:74662200-74677200	Weak transcription	Thymus	Thymus
19	chr11:74662200-74677800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:74662200-74677800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
22	chr11:74662400-74670800	Weak transcription	HUVEC	blood vessel
23	chr11:74662400-74671000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:74662400-74673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:74662400-74675200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:74662400-74677800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:74662400-74677800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:74662400-74677800	Weak transcription	Fetal Stomach	stomach
29	chr11:74662400-74680600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:74662400-74691400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:74662600-74670400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:74662600-74676600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:74662600-74682800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:74662600-74686000	Weak transcription	Fetal Brain Male	brain
35	chr11:74662800-74670400	Weak transcription	Spleen	Spleen
36	chr11:74662800-74677800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:74662800-74682200	Weak transcription	Lung	lung
38	chr11:74663000-74669400	Strong transcription	Hela-S3	cervix
39	chr11:74663000-74671000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr11:74663200-74680000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr11:74663600-74669400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:74663600-74671800	Weak transcription	Fetal Brain Female	brain
43	chr11:74664000-74671000	Strong transcription	NHEK	skin
44	chr11:74664000-74680400	Weak transcription	HMEC	breast
45	chr11:74664200-74671600	Weak transcription	NH-A	brain
46	chr11:74664200-74677200	Weak transcription	Fetal Lung	lung
47	chr11:74664400-74675800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr11:74664400-74678000	Weak transcription	Brain Germinal Matrix	brain
49	chr11:74664600-74669800	Strong transcription	Primary hematopoietic stem cells	blood
50	chr11:74664600-74670800	Strong transcription	Primary T cells fromperipheralblood	blood

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