Variant report

Variant	rs1048076
Chromosome Location	chr6:46112372-46112373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:46110640..46112825-chr6:46112958..46115144,2	K562	blood:
2	chr6:46112224..46114185-chr6:46116270..46118117,2	K562	blood:
3	chr6:46107057..46110054-chr6:46111949..46114711,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1011370	0.82[CEU][hapmap]
rs1048079	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1048082	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076736	1.00[YRI][hapmap]
rs1076737	1.00[YRI][hapmap]
rs1076738	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs10807334	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10948283	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11754760	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12196107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12215921	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12526912	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13210366	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs14781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143747	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2206965	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2206968	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2223777	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2223778	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2235881	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2235883	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295016	0.82[AFR][1000 genomes]
rs2295017	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2295018	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2894662	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3756802	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756803	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806994	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806995	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3891763	0.82[AFR][1000 genomes]
rs3905440	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458490	0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458491	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458492	0.82[AFR][1000 genomes]
rs6921826	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs6923745	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6926570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6941587	0.82[AFR][1000 genomes]
rs71544217	0.81[AMR][1000 genomes]
rs71566566	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7357078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7451713	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7740398	1.00[YRI][hapmap]
rs7748442	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7748469	0.83[EUR][1000 genomes]
rs7754582	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7769738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7773230	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7775082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180644	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs872859	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs910179	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349348	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357501	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357502	0.81[AFR][1000 genomes]
rs9367233	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9367234	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9367237	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369599	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369601	0.82[AFR][1000 genomes]
rs9381430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395156	0.80[GIH][hapmap]
rs9395158	0.86[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395159	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9463185	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472694	0.85[AMR][1000 genomes]
rs9472698	0.82[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472699	0.84[AFR][1000 genomes]
rs9472700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9472704	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9472705	0.81[AFR][1000 genomes]
rs9472707	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9472708	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9472709	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9472713	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9472714	1.00[YRI][hapmap]
rs9472715	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs995564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022912	chr6:46093409-46116449	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	esv1842212	chr6:46111940-46127836	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1048076	ENPP5	cis	Thyroid	GTEx
rs1048076	ENPP5	cis	parietal	SCAN
rs1048076	ENPP5	cis	cerebellum	SCAN
rs1048076	MBOAT4	trans	cerebellum	SCAN
rs1048076	ZNF318	cis	parietal	SCAN
rs1048076	CLIC5	cis	parietal	SCAN
rs1048076	ENPP4	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46098800-46112400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr6:46098800-46112800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:46098800-46112800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:46098800-46112800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:46098800-46113000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:46098800-46117800	Weak transcription	Gastric	stomach
7	chr6:46098800-46129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:46101800-46113000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:46102200-46113000	Weak transcription	Fetal Intestine Large	intestine
10	chr6:46105000-46114600	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:46105400-46115000	Weak transcription	Aorta	Aorta
12	chr6:46105400-46133800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:46105600-46113200	Weak transcription	Spleen	Spleen
14	chr6:46105600-46128600	Weak transcription	Brain Angular Gyrus	brain
15	chr6:46105600-46137400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:46105800-46112800	Weak transcription	HSMMtube	muscle
17	chr6:46106400-46112600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:46106400-46112800	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:46106400-46125400	Weak transcription	Psoas Muscle	Psoas
20	chr6:46106400-46138000	Weak transcription	Lung	lung
21	chr6:46106600-46112800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:46106600-46112800	Weak transcription	Liver	Liver
23	chr6:46107800-46114000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:46108000-46130000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:46108800-46112600	Weak transcription	Ovary	ovary
26	chr6:46109600-46112400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:46109800-46112400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:46110200-46112400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr6:46110400-46112800	Enhancers	Fetal Heart	heart
30	chr6:46110600-46112800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr6:46110600-46112800	Strong transcription	Dnd41	blood
32	chr6:46110800-46112400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:46111200-46114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:46111400-46112400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:46111400-46113000	Weak transcription	Left Ventricle	heart
36	chr6:46111400-46113000	Weak transcription	Thymus	Thymus
37	chr6:46111400-46113200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:46111400-46113800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:46111400-46114200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:46111400-46114200	Weak transcription	GM12878-XiMat	blood
41	chr6:46111400-46114800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:46111400-46115200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:46111400-46116200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:46111400-46117200	Weak transcription	Brain Anterior Caudate	brain
45	chr6:46111400-46125200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:46111400-46128600	Weak transcription	Primary T cells from cord blood	blood
47	chr6:46111400-46128800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr6:46111400-46137800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:46111600-46116600	Weak transcription	Primary B cells from cord blood	blood
50	chr6:46111600-46116600	Weak transcription	Rectal Mucosa Donor 31	rectum

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