Variant report

Variant	rs239224
Chromosome Location	chr6:101111120-101111121
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101103606..101105187-chr6:101110691..101113240,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11964230	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17054273	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs171257	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs183023	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2201495	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239214	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs239220	0.86[EUR][1000 genomes]
rs239233	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239243	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239244	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2398133	1.00[AMR][1000 genomes]
rs240122	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240144	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240155	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs240157	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs240165	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs240166	1.00[AMR][1000 genomes]
rs240768	1.00[CEU][hapmap]
rs240777	1.00[AMR][1000 genomes]
rs240782	1.00[AMR][1000 genomes]
rs240785	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs33988845	0.94[AMR][1000 genomes]
rs401864	0.80[CEU][hapmap]
rs412177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4240588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6927313	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72939355	1.00[AMR][1000 genomes]
rs72941252	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72942932	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72942958	1.00[EUR][1000 genomes]
rs72942985	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72942988	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72942989	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72949504	0.94[AMR][1000 genomes]
rs9373580	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9689068	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv886454	chr6:101049108-101123503	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv886455	chr6:101049108-101203051	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
14	nsv886456	chr6:101049108-101277926	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv463990	chr6:101058886-101123503	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv604269	chr6:101058886-101123503	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv604270	chr6:101058886-101196080	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv604271	chr6:101072307-101158950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv463991	chr6:101072307-101196080	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv604272	chr6:101072307-101196080	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv463992	chr6:101072307-101197953	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
22	nsv604273	chr6:101072307-101197953	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
23	nsv604274	chr6:101078718-101196080	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	nsv1027288	chr6:101091434-101121237	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv1032826	chr6:101091434-101147095	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv1028583	chr6:101091434-101152631	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv1015465	chr6:101091434-101157493	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv1031817	chr6:101091995-101157493	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs239224	GRIK2	cis	Artery Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101071600-101127800	Weak transcription	Hela-S3	cervix
2	chr6:101093000-101111600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:101093000-101112400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:101093000-101145800	Weak transcription	Fetal Thymus	thymus
5	chr6:101099400-101116600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:101100200-101118000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:101100400-101111200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:101100400-101131400	Weak transcription	Liver	Liver
9	chr6:101100600-101111200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:101100600-101149800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:101100800-101117800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:101100800-101118000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:101100800-101122400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:101100800-101124400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:101100800-101126600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:101100800-101129200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:101100800-101147600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr6:101100800-101164600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:101101400-101120800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:101103000-101112600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:101103200-101118000	Weak transcription	Primary B cells from cord blood	blood
22	chr6:101103800-101121400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:101103800-101126600	Weak transcription	Placenta	Placenta
24	chr6:101103800-101129400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:101103800-101129600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:101103800-101143600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:101104000-101135000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr6:101109600-101112000	Strong transcription	Dnd41	blood
29	chr6:101110000-101111600	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr6:101110000-101118000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:101110000-101147600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:101110200-101111800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:101110200-101112000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr6:101110200-101112400	Weak transcription	GM12878-XiMat	blood
35	chr6:101110200-101113000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr6:101110400-101111600	Enhancers	NHDF-Ad	bronchial
37	chr6:101110400-101119000	Weak transcription	Left Ventricle	heart
38	chr6:101110400-101146800	Weak transcription	Primary T cells from cord blood	blood
39	chr6:101110600-101111800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr6:101110600-101112000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:101110600-101112000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:101110600-101112000	Enhancers	HMEC	breast
43	chr6:101110600-101112200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:101110600-101112800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr6:101110800-101111200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:101110800-101111400	Enhancers	H9 Cell Line	embryonic stem cell
47	chr6:101110800-101111600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr6:101110800-101111600	Enhancers	HSMMtube	muscle
49	chr6:101110800-101111800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:101110800-101111800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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