Variant report

Variant	rs3020213
Chromosome Location	chr8:6369930-6369931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11776519	0.86[CEU][hapmap]
rs13250387	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13277236	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13278243	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13281117	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17077317	0.86[CEU][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1870	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1961222	0.83[CEU][hapmap]
rs1975616	0.95[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap]
rs2167071	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2442468	0.88[CHD][hapmap]
rs2442629	0.82[ASN][1000 genomes]
rs2442631	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2442632	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs2442633	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.96[ASN][1000 genomes]
rs2442634	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2442635	0.91[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.94[ASN][1000 genomes]
rs2442636	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2515420	0.92[ASN][1000 genomes]
rs2515421	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2515422	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2515424	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2515435	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2515441	0.87[ASN][1000 genomes]
rs2916702	1.00[CEU][hapmap]
rs2916715	0.82[CEU][hapmap]
rs2916724	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2916725	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2916726	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2916729	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916731	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916735	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2916736	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2916747	0.97[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2916755	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2916756	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2922804	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap]
rs2922895	0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2922897	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2922900	0.81[CEU][hapmap]
rs2922901	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2922903	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922905	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2922906	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922907	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2959790	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2959791	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2959793	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs2979671	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2979672	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2979673	0.86[CEU][hapmap]
rs3020210	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs3020212	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3020214	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3020216	0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020217	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3020218	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3020219	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3020221	0.88[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35948012	0.82[AMR][1000 genomes];0.83[EUR][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	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv890057	chr8:6317165-6427868	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv1022895	chr8:6355213-6414874	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv933260	chr8:6357124-6410013	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking 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	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3020213	XKR5	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6308000-6372600	Weak transcription	HMEC	breast
2	chr8:6317800-6380200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr8:6325800-6374400	Weak transcription	K562	blood
4	chr8:6336800-6377600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr8:6338800-6389600	Weak transcription	HSMMtube	muscle
6	chr8:6340400-6371600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr8:6340800-6371800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr8:6341000-6372000	Weak transcription	A549	lung
9	chr8:6341000-6375000	Weak transcription	Brain Angular Gyrus	brain
10	chr8:6341200-6371200	Weak transcription	Fetal Brain Female	brain
11	chr8:6342400-6421400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr8:6345800-6402400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:6346200-6386000	Weak transcription	NH-A	brain
14	chr8:6352000-6375600	Weak transcription	Aorta	Aorta
15	chr8:6352400-6391400	Weak transcription	Ovary	ovary
16	chr8:6352600-6372800	Weak transcription	Brain Substantia Nigra	brain
17	chr8:6354600-6370600	Weak transcription	Small Intestine	intestine
18	chr8:6355600-6372800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr8:6355800-6373000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr8:6357800-6391400	Weak transcription	Colonic Mucosa	Colon
21	chr8:6359000-6374800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr8:6359200-6374000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr8:6359200-6389200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr8:6360400-6386200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr8:6360600-6373800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr8:6360800-6371800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr8:6360800-6383800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:6361200-6372000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr8:6361200-6372800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr8:6361200-6372800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr8:6361200-6375200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr8:6361200-6375800	Weak transcription	Right Ventricle	heart
33	chr8:6361200-6378000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr8:6361200-6380800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:6361200-6386000	Weak transcription	Fetal Intestine Large	intestine
36	chr8:6361400-6372600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr8:6361400-6372600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr8:6361400-6372800	Weak transcription	Brain Anterior Caudate	brain
39	chr8:6361400-6380000	Weak transcription	Colon Smooth Muscle	Colon
40	chr8:6361600-6371200	Weak transcription	Adipose Nuclei	Adipose
41	chr8:6362400-6372600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr8:6362600-6378200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr8:6364200-6372200	Weak transcription	Fetal Muscle Leg	muscle
44	chr8:6364200-6372800	Weak transcription	Pancreas	Pancrea
45	chr8:6364200-6377200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr8:6364200-6417200	Weak transcription	Fetal Kidney	kidney
47	chr8:6364200-6478200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr8:6364800-6373000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr8:6365400-6370800	Strong transcription	Dnd41	blood
50	chr8:6365800-6372400	Weak transcription	Fetal Heart	heart

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