Variant report

Variant	rs2044643
Chromosome Location	chr8:59810308-59810309
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10093993	0.81[EUR][1000 genomes]
rs10098750	0.81[EUR][1000 genomes]
rs10108037	0.81[EUR][1000 genomes]
rs10109566	0.81[YRI][hapmap]
rs1015794	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12543935	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs12675191	0.87[ASN][1000 genomes]
rs13261666	0.81[EUR][1000 genomes]
rs13262230	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13263261	0.81[EUR][1000 genomes]
rs13268621	0.81[EUR][1000 genomes]
rs13271523	0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs13280926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1349113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375192	0.82[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs1375193	0.82[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1448541	0.81[EUR][1000 genomes]
rs1448547	0.83[JPT][hapmap]
rs1448549	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs16924227	0.83[YRI][hapmap]
rs17299611	0.83[JPT][hapmap]
rs1900774	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2197803	0.82[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs2326213	0.81[EUR][1000 genomes]
rs2326268	0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3780001	0.84[CHD][hapmap]
rs4527857	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs4527858	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs4737525	0.81[YRI][hapmap]
rs4737526	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4737527	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4737528	0.83[YRI][hapmap]
rs4738729	0.81[EUR][1000 genomes]
rs4738730	0.81[EUR][1000 genomes]
rs4738731	0.84[CHD][hapmap];0.80[EUR][1000 genomes]
rs4738732	0.84[CHD][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs4738733	0.81[EUR][1000 genomes]
rs4738736	0.82[ASN][1000 genomes]
rs6415583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6471757	0.81[YRI][hapmap]
rs66954327	0.84[ASN][1000 genomes]
rs6983623	0.82[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs6983967	0.82[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs6985104	0.81[LWK][hapmap]
rs6988143	0.81[EUR][1000 genomes]
rs7000535	0.80[TSI][hapmap];0.81[YRI][hapmap]
rs7001367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7012303	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap]
rs7813733	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs7829715	0.80[TSI][hapmap];0.81[YRI][hapmap]
rs7834158	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7845800	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9298002	0.80[EUR][1000 genomes]

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	nsv526468	chr8:59799820-59813809	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2044643	GRIK4	trans	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59771400-59811000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr8:59790800-59811200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr8:59791400-59811000	Weak transcription	Brain Angular Gyrus	brain
4	chr8:59794200-59820000	Weak transcription	Fetal Intestine Large	intestine
5	chr8:59794800-59811000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr8:59800800-59810600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr8:59800800-59811000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr8:59801400-59811000	Weak transcription	Primary T cells from cord blood	blood
9	chr8:59802200-59810800	Weak transcription	HUVEC	blood vessel
10	chr8:59802800-59826600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr8:59804200-59811000	Weak transcription	Gastric	stomach
12	chr8:59805000-59812200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr8:59805000-59815200	Weak transcription	Fetal Heart	heart
14	chr8:59805200-59815600	Weak transcription	Fetal Stomach	stomach
15	chr8:59805400-59810600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr8:59805400-59826800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr8:59805600-59811000	Weak transcription	NHDF-Ad	bronchial
18	chr8:59806000-59814000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr8:59806400-59815400	Weak transcription	Colon Smooth Muscle	Colon
20	chr8:59808400-59811400	Enhancers	Fetal Brain Male	brain
21	chr8:59808600-59815200	Weak transcription	Osteobl	bone
22	chr8:59809000-59826400	Weak transcription	Thymus	Thymus
23	chr8:59809200-59810800	Weak transcription	Dnd41	blood
24	chr8:59809600-59810400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr8:59809800-59811800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr8:59810000-59810400	Weak transcription	Fetal Brain Female	brain
27	chr8:59810200-59811000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr8:59810200-59811000	Weak transcription	Fetal Thymus	thymus
29	chr8:59810200-59814800	Weak transcription	Brain Germinal Matrix	brain

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