Variant report

Variant	rs171257
Chromosome Location	chr6:101048197-101048198
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11964230	0.89[AMR][1000 genomes]
rs17054273	0.89[AMR][1000 genomes]
rs17245494	0.82[EUR][1000 genomes]
rs183023	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2201495	0.89[AMR][1000 genomes]
rs239192	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs239200	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs239205	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs239214	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs239224	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs239233	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs239243	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs239244	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2398133	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240122	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240144	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240155	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs240157	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs240165	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs240166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240768	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs240777	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240779	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs240782	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240785	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3213542	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs33988845	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs401864	0.80[CEU][hapmap]
rs412177	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4240588	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6927313	0.89[AMR][1000 genomes]
rs6931919	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72939355	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72941252	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72942932	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72942958	0.85[EUR][1000 genomes]
rs72942985	0.89[AMR][1000 genomes]
rs72942988	0.89[AMR][1000 genomes]
rs72942989	0.89[AMR][1000 genomes]
rs72949504	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9373580	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9689068	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv886444	chr6:100961198-101084946	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv604263	chr6:100980874-101078718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv463986	chr6:100995048-101084946	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv604264	chr6:100995048-101084946	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1028016	chr6:101001055-101158822	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv886445	chr6:101004751-101240763	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv886446	chr6:101018032-101084946	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv886447	chr6:101018032-101091434	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv886448	chr6:101018032-101123503	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv886449	chr6:101018032-101147095	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv886450	chr6:101018032-101168137	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv886451	chr6:101018032-101172328	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv886452	chr6:101018032-101192051	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv886453	chr6:101018032-101203051	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv463987	chr6:101036713-101078718	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv604265	chr6:101036713-101078718	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv470848	chr6:101036713-101102584	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv463988	chr6:101036713-101158950	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv604266	chr6:101036713-101158950	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv463989	chr6:101039215-101078718	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv604267	chr6:101039215-101078718	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv1840320	chr6:101039215-101102585	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs171257	GRIK2	cis	Artery Tibial	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101009000-101065600	Weak transcription	NHEK	skin
2	chr6:101011000-101080800	Weak transcription	HepG2	liver
3	chr6:101015800-101049200	Weak transcription	Esophagus	oesophagus
4	chr6:101016400-101065800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:101017200-101069400	Weak transcription	Fetal Lung	lung
6	chr6:101017800-101069800	Weak transcription	Lung	lung
7	chr6:101018400-101051200	Weak transcription	Right Ventricle	heart
8	chr6:101020400-101066200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:101025800-101099800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:101027800-101049600	Weak transcription	Fetal Kidney	kidney
11	chr6:101027800-101070000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:101028000-101068800	Weak transcription	Psoas Muscle	Psoas
13	chr6:101030200-101070000	Weak transcription	Aorta	Aorta
14	chr6:101031200-101048600	Weak transcription	Brain Anterior Caudate	brain
15	chr6:101032400-101102000	Weak transcription	Thymus	Thymus
16	chr6:101032400-101104400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:101032600-101102000	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:101032600-101110400	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:101032800-101065600	Weak transcription	Colonic Mucosa	Colon
20	chr6:101033000-101048600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:101033400-101048400	Weak transcription	HUVEC	blood vessel
22	chr6:101033600-101057600	Weak transcription	Brain Angular Gyrus	brain
23	chr6:101033800-101065400	Weak transcription	Hela-S3	cervix
24	chr6:101034000-101085000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:101034400-101066200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:101034400-101084200	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:101034400-101092400	Weak transcription	Pancreas	Pancrea
28	chr6:101034600-101048800	Weak transcription	Left Ventricle	heart
29	chr6:101034600-101048800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:101034600-101055000	Weak transcription	Fetal Intestine Small	intestine
31	chr6:101035400-101048200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:101035400-101065600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:101035800-101070000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:101036000-101064600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:101036000-101075200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:101036000-101084800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:101036200-101053400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:101036200-101073000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:101036200-101084000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:101036600-101048200	Weak transcription	Brain Substantia Nigra	brain
41	chr6:101037400-101110600	Weak transcription	K562	blood
42	chr6:101037600-101048200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:101037600-101048600	Weak transcription	HMEC	breast
44	chr6:101037600-101052400	Weak transcription	Fetal Intestine Large	intestine
45	chr6:101037600-101054000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:101037600-101056400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:101037600-101057000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr6:101037600-101071200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:101037600-101072200	Weak transcription	Adipose Nuclei	Adipose
50	chr6:101037800-101107200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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