Variant report

Variant	rs4985955
Chromosome Location	chr17:20898014-20898015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20895064..20900549-chr17:20901410..20906180,6	K562	blood:
2	chr17:20895463..20898047-chr17:20898321..20900254,2	K562	blood:
3	chr17:20896404..20898523-chr17:20904680..20906876,2	K562	blood:

Variant related genes	Relation type
ENSG00000263986	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1038107	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1038109	0.82[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1044410	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1044414	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1044420	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204326	0.91[ASW][hapmap]
rs11204328	0.86[ASN][1000 genomes]
rs11204330	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1127815	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11650829	0.86[ASN][1000 genomes]
rs11651632	0.86[ASN][1000 genomes]
rs11654347	0.85[ASN][1000 genomes]
rs11654680	0.85[ASN][1000 genomes]
rs11655364	0.85[ASN][1000 genomes]
rs11658914	0.85[ASN][1000 genomes]
rs11659113	0.82[ASN][1000 genomes]
rs11871167	0.85[ASN][1000 genomes]
rs12103803	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12150138	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12600604	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12936249	0.85[ASN][1000 genomes]
rs1531567	0.85[ASN][1000 genomes]
rs1904230	0.80[AMR][1000 genomes]
rs1993901	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2009756	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2127094	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291037	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2364327	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2364328	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2364329	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2364330	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2364331	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2364332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2364333	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28419675	0.86[ASN][1000 genomes]
rs28595150	0.85[ASN][1000 genomes]
rs3612	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816664	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3943299	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4462662	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4613123	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985813	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985820	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985824	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4985935	0.86[JPT][hapmap]
rs4985941	0.95[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985946	0.85[ASN][1000 genomes]
rs4985947	0.85[ASN][1000 genomes]
rs4985948	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985949	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985952	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985954	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985957	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985962	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985964	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985973	0.84[AMR][1000 genomes]
rs4985974	0.95[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs5005801	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55730423	0.86[ASN][1000 genomes]
rs55749232	0.85[ASN][1000 genomes]
rs55985304	0.85[ASN][1000 genomes]
rs62056767	0.82[ASN][1000 genomes]
rs6587109	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587115	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6650606	0.86[ASN][1000 genomes]
rs6650607	0.86[ASN][1000 genomes]
rs7207724	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7207753	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7208779	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7211094	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap]
rs7213253	0.86[ASN][1000 genomes]
rs7213684	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7215369	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7216090	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216449	0.82[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7216786	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7216978	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7218112	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7218443	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7219244	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7220023	0.86[ASN][1000 genomes]
rs7221483	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7221757	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7223388	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7224746	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7226229	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8064435	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8071311	0.86[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]
rs8075790	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs8076078	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8082210	0.85[ASN][1000 genomes]
rs880652	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs880654	0.86[ASN][1000 genomes]
rs899334	0.86[ASN][1000 genomes]
rs899335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899338	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899341	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs899342	0.95[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs961004	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9797279	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9895047	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9896259	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9896301	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9896416	0.86[ASN][1000 genomes]
rs9897434	0.85[ASN][1000 genomes]
rs9898265	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9902303	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs996065	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4985955	FAM27L	cis	cerebellum	SCAN
rs4985955	SLC5A10	cis	parietal	SCAN
rs4985955	USP22	cis	Whole Blood	GTEx
rs4985955	PEMT	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20893000-20901600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:20893800-20901200	Weak transcription	Right Atrium	heart
3	chr17:20894800-20899000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:20896400-20898400	Enhancers	Stomach Mucosa	stomach
5	chr17:20896400-20900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:20896400-20901400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:20896400-20901600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:20896400-20902800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:20896600-20898200	Enhancers	Spleen	Spleen
10	chr17:20896600-20901800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:20896600-20901800	Weak transcription	HUVEC	blood vessel
12	chr17:20896600-20902000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr17:20896600-20906800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr17:20896800-20899400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:20896800-20899400	Weak transcription	Right Ventricle	heart
16	chr17:20896800-20899600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:20896800-20900000	Weak transcription	Adipose Nuclei	Adipose
18	chr17:20896800-20900000	Weak transcription	Fetal Muscle Leg	muscle
19	chr17:20896800-20900600	Weak transcription	Esophagus	oesophagus
20	chr17:20896800-20900600	Weak transcription	Fetal Intestine Small	intestine
21	chr17:20896800-20900600	Weak transcription	Left Ventricle	heart
22	chr17:20896800-20900800	Weak transcription	Brain Germinal Matrix	brain
23	chr17:20896800-20900800	Weak transcription	Fetal Brain Female	brain
24	chr17:20896800-20901000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:20896800-20901000	Weak transcription	Ovary	ovary
26	chr17:20896800-20901400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:20896800-20901400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr17:20896800-20901400	Weak transcription	Fetal Lung	lung
29	chr17:20896800-20901600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:20896800-20901600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:20896800-20901600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr17:20896800-20901600	Weak transcription	HSMM	muscle
33	chr17:20896800-20901800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr17:20896800-20901800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr17:20896800-20901800	Weak transcription	NHDF-Ad	bronchial
36	chr17:20896800-20902200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr17:20896800-20902200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:20896800-20902200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:20896800-20902200	Weak transcription	Fetal Thymus	thymus
40	chr17:20896800-20902400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr17:20896800-20902600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr17:20896800-20902600	Weak transcription	Colonic Mucosa	Colon
43	chr17:20896800-20902600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr17:20896800-20902600	Weak transcription	NHEK	skin
45	chr17:20896800-20904200	Weak transcription	Primary T cells from cord blood	blood
46	chr17:20896800-20904800	Weak transcription	Fetal Kidney	kidney
47	chr17:20896800-20905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:20897000-20898200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr17:20897000-20899400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr17:20897000-20899600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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