Variant report

Variant	rs263114
Chromosome Location	chr6:142882955-142882956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1070576	0.93[ASN][1000 genomes]
rs1070577	0.93[ASN][1000 genomes]
rs1098071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217677	0.85[ASN][1000 genomes]
rs166401	0.86[EUR][1000 genomes]
rs171913	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171914	0.95[ASN][1000 genomes]
rs183799	0.86[EUR][1000 genomes]
rs187810	0.90[EUR][1000 genomes]
rs190522	0.86[EUR][1000 genomes]
rs190523	0.86[EUR][1000 genomes]
rs196353	0.88[EUR][1000 genomes]
rs263103	0.87[EUR][1000 genomes]
rs263104	0.87[EUR][1000 genomes]
rs263105	0.87[EUR][1000 genomes]
rs263107	0.87[EUR][1000 genomes]
rs263113	0.90[EUR][1000 genomes]
rs263115	0.88[EUR][1000 genomes]
rs263116	0.90[EUR][1000 genomes]
rs263119	0.88[EUR][1000 genomes]
rs263120	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263121	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263122	0.86[EUR][1000 genomes]
rs263154	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs263155	0.85[EUR][1000 genomes]
rs263156	0.85[EUR][1000 genomes]
rs263165	0.88[EUR][1000 genomes]
rs263166	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263167	0.87[EUR][1000 genomes]
rs263168	0.86[EUR][1000 genomes]
rs263171	0.86[EUR][1000 genomes]
rs263172	0.84[EUR][1000 genomes]
rs263174	0.86[EUR][1000 genomes]
rs263175	0.94[ASN][1000 genomes]
rs263176	0.85[EUR][1000 genomes]
rs2664050	0.93[ASN][1000 genomes]
rs605790	0.89[EUR][1000 genomes]
rs6906209	0.86[ASN][1000 genomes]
rs702289	0.94[ASN][1000 genomes]
rs702290	0.94[ASN][1000 genomes]
rs702291	0.94[ASN][1000 genomes]
rs702292	0.98[ASN][1000 genomes]
rs702293	0.98[ASN][1000 genomes]
rs702294	0.91[ASN][1000 genomes]
rs702295	0.96[ASN][1000 genomes]
rs702296	0.96[ASN][1000 genomes]
rs702298	0.93[ASN][1000 genomes]
rs839554	0.85[EUR][1000 genomes]
rs839556	0.85[EUR][1000 genomes]
rs863432	0.94[ASN][1000 genomes]
rs9390007	0.84[ASN][1000 genomes]
rs9390009	0.85[ASN][1000 genomes]
rs9496420	0.86[ASN][1000 genomes]
rs9496432	0.90[JPT][hapmap]

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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	nsv1023426	chr6:142813845-142940262	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830827	chr6:142840734-143015005	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv520479	chr6:142869099-142908146	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs263114	GRM1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142873600-142888800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:142881800-142884200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr6:142881800-142884400	Enhancers	Primary T cells from cord blood	blood
4	chr6:142882000-142883400	Enhancers	Dnd41	blood
5	chr6:142882000-142883800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:142882000-142884000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr6:142882000-142884200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:142882000-142884200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:142882000-142884400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:142882200-142883600	Enhancers	Fetal Thymus	thymus
11	chr6:142882200-142884000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:142882200-142884200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr6:142882400-142883000	Enhancers	Thymus	Thymus
14	chr6:142882400-142884200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:142882600-142889400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:142882800-142883400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:142882800-142884200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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