Variant report

Variant	rs6658861
Chromosome Location	chr1:174857981-174857982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174849949..174852627-chr1:174855691..174858131,3	K562	blood:
2	chr1:174857903..174859403-chr1:174868929..174871590,2	K562	blood:
3	chr1:174856455..174858705-chr1:174861432..174864303,3	K562	blood:

Variant related genes	Relation type
ENSG00000237249	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10465483	0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap]
rs10912870	0.80[CHD][hapmap]
rs1653626	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs1653627	0.86[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs1653632	0.85[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs16847633	0.80[CHD][hapmap]
rs170768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1754351	0.86[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs1754355	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs1793291	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1793293	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1793297	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs1793319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894200	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2187562	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs2987869	0.86[ASW][hapmap];0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap]
rs2987874	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs3018410	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs3118980	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs3133270	0.85[CEU][hapmap]
rs332783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs332795	0.86[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs332796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs332799	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs333418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4233195	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs4650666	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4651238	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs6425305	0.82[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs6665216	0.82[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs6688577	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538588	0.82[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs7538650	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs913685	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9804056	0.82[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]

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	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6658861	GPR52	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174844800-174871600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:174844800-174874400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:174844800-174877400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:174845000-174862800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:174845000-174863000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:174845200-174862600	Weak transcription	Liver	Liver
7	chr1:174846200-174861200	Weak transcription	GM12878-XiMat	blood
8	chr1:174846600-174862800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:174846800-174861000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:174846800-174874000	Weak transcription	Ovary	ovary
11	chr1:174847000-174869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:174847400-174862800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:174847400-174863000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:174847400-174864400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:174847400-174864600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:174847400-174864600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:174847600-174874400	Weak transcription	Esophagus	oesophagus
18	chr1:174849200-174858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:174849200-174864400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:174849600-174864400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:174850200-174861200	Weak transcription	Pancreas	Pancrea
22	chr1:174850200-174874800	Weak transcription	Fetal Stomach	stomach
23	chr1:174850400-174869600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:174852000-174873400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:174852800-174859000	Weak transcription	Gastric	stomach
26	chr1:174852800-174860600	Weak transcription	Left Ventricle	heart
27	chr1:174852800-174864000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:174852800-174874800	Weak transcription	Spleen	Spleen
29	chr1:174853000-174858800	Weak transcription	K562	blood
30	chr1:174853000-174859000	Weak transcription	HepG2	liver
31	chr1:174853400-174865000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:174853400-174870200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:174854000-174862800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:174854200-174859000	Weak transcription	Stomach Mucosa	stomach
35	chr1:174854200-174859200	Weak transcription	Fetal Heart	heart
36	chr1:174854200-174862800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:174855400-174861200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:174855600-174862400	Weak transcription	Small Intestine	intestine
39	chr1:174855800-174861200	Weak transcription	Fetal Intestine Large	intestine
40	chr1:174856200-174860800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:174856400-174862600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:174856600-174866600	Weak transcription	Primary B cells from cord blood	blood
43	chr1:174856800-174859000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:174856800-174876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:174857000-174870800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:174857000-174871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:174857200-174858600	Strong transcription	Fetal Intestine Small	intestine
48	chr1:174857800-174867200	Weak transcription	Primary B cells from peripheral blood	blood

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