Variant report

Variant	rs6671872
Chromosome Location	chr1:213318765-213318766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10127851	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10465694	0.88[EUR][1000 genomes]
rs10864034	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10864036	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10864038	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120082	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs1391549	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1391550	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1498357	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1566247	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17020338	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1976333	0.88[EUR][1000 genomes]
rs1995151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2132428	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs2173398	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2494767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2647387	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2817976	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2817978	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817981	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2817984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2841425	0.89[ASN][1000 genomes]
rs2841427	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2841439	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3002285	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3010779	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap]
rs3010780	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs3010787	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs3124668	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs4655386	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4951476	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes]
rs4951479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4951662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs4951677	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6419469	0.83[AMR][1000 genomes]
rs6419470	0.90[AMR][1000 genomes]
rs6540778	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6540780	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6540781	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540782	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658259	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6666814	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6679510	0.86[EUR][1000 genomes]
rs6691488	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6692056	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6692144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6693291	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6697921	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs6699158	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6700169	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7517229	0.80[EUR][1000 genomes]
rs7535369	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7547274	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308430	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9429901	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9429902	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9430118	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9430120	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9430121	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9430122	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9430123	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392967	chr1:213271844-213490132	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv508692	chr1:213309036-213330907	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv14011	chr1:213314571-213320124	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv1825966	chr1:213316089-213319599	Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv1827995	chr1:213316089-213319599	Strong transcription ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv1831424	chr1:213316089-213319599	Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1832704	chr1:213316089-213319599	Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv549178	chr1:213316089-213319599	Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv1830404	chr1:213316089-213320011	Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv1830707	chr1:213316089-213320011	Strong transcription Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv1830896	chr1:213316089-213320011	Strong transcription Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv1832653	chr1:213316089-213320011	ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv1832323	chr1:213316408-213319010	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6671872	ANGEL2	cis	parietal	SCAN
rs6671872	RPS6KC1	cis	Artery Tibial	GTEx
rs6671872	SNORA16B	cis	cerebellum	SCAN
rs6671872	BATF3	cis	parietal	SCAN
rs6671872	ANGEL2	cis	Esophagus Mucosa	GTEx
rs6671872	ANGEL2	cis	cerebellum	SCAN
rs6671872	KCNH1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213261600-213327400	Weak transcription	Aorta	Aorta
2	chr1:213281200-213320400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:213284600-213349800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr1:213294200-213321400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:213297400-213320400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:213301000-213371000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:213301000-213374800	Weak transcription	HSMM	muscle
8	chr1:213302600-213358200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:213306200-213331600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:213306600-213323400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:213307200-213319200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:213309600-213329000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:213309600-213336000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:213309800-213319600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:213310000-213345800	Weak transcription	Lung	lung
16	chr1:213310000-213370400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:213310400-213333600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:213310400-213345800	Weak transcription	Ovary	ovary
19	chr1:213312000-213340200	Weak transcription	HSMMtube	muscle
20	chr1:213312200-213340000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:213312200-213343600	Weak transcription	HepG2	liver
22	chr1:213312400-213322200	Weak transcription	Fetal Lung	lung
23	chr1:213312400-213336000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:213312600-213326800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:213312600-213327400	Weak transcription	K562	blood
26	chr1:213313000-213320600	Weak transcription	NHDF-Ad	bronchial
27	chr1:213313000-213320800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:213313400-213322200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:213313800-213336000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:213314000-213320200	Weak transcription	Primary B cells from cord blood	blood
31	chr1:213314600-213319200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:213316000-213340000	Weak transcription	Psoas Muscle	Psoas
33	chr1:213316200-213328400	Weak transcription	Placenta	Placenta
34	chr1:213316400-213320200	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:213316400-213336200	Weak transcription	NH-A	brain
36	chr1:213317200-213320000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:213317200-213320200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:213317400-213349600	Weak transcription	Left Ventricle	heart
39	chr1:213317600-213318800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:213317600-213322600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:213317800-213319600	Weak transcription	Fetal Intestine Large	intestine
42	chr1:213317800-213331000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:213317800-213351600	Weak transcription	Fetal Kidney	kidney
44	chr1:213318200-213322000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:213318600-213319000	Strong transcription	Primary monocytes fromperipheralblood	blood

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