Variant report

Variant	rs839556
Chromosome Location	chr6:142871878-142871879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1098071	0.85[EUR][1000 genomes]
rs166401	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs171913	0.87[EUR][1000 genomes]
rs183799	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187810	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs190522	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs190523	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs196353	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2077836	0.84[EUR][1000 genomes]
rs263103	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs263104	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263105	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263107	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263113	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs263114	0.85[EUR][1000 genomes]
rs263115	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs263116	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs263119	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs263120	0.83[EUR][1000 genomes]
rs263121	0.83[EUR][1000 genomes]
rs263122	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs263130	0.84[EUR][1000 genomes]
rs263154	0.82[EUR][1000 genomes]
rs263155	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs263156	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs263165	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs263166	0.83[EUR][1000 genomes]
rs263167	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263168	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263171	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263172	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs263174	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs263176	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs605790	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839554	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

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
rs839556	GRM1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142864400-142872000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:142864400-142872000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:142864400-142872000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:142864400-142872200	Weak transcription	NHEK	skin
5	chr6:142869400-142872200	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr6:142869400-142872400	Enhancers	Primary T cells from cord blood	blood
7	chr6:142869400-142872800	Enhancers	Dnd41	blood
8	chr6:142869600-142873200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr6:142871000-142872200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:142871000-142872600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:142871000-142873200	Enhancers	HSMMtube	muscle
12	chr6:142871400-142872600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:142871400-142872800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:142871400-142873000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:142871400-142873200	Enhancers	Fetal Stomach	stomach
16	chr6:142871400-142873200	Enhancers	HSMM	muscle
17	chr6:142871400-142873400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:142871600-142872000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr6:142871600-142872000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr6:142871600-142872200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:142871600-142872400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:142871600-142873200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:142871600-142873600	Enhancers	Fetal Lung	lung
24	chr6:142871800-142872000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:142871800-142872200	Enhancers	HMEC	breast
26	chr6:142871800-142872400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr6:142871800-142872800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr6:142871800-142873000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr6:142871800-142873000	Enhancers	Fetal Muscle Leg	muscle
30	chr6:142871800-142873000	Enhancers	Fetal Thymus	thymus

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