Variant report

Variant	rs4767685
Chromosome Location	chr12:118974349-118974350
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10850988	0.81[AMR][1000 genomes]
rs10850989	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10850990	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10850992	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11068983	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12304368	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12307358	0.92[AMR][1000 genomes]
rs12366746	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12366749	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57244588	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6490191	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7306583	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7309801	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7315333	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7486459	0.87[AMR][1000 genomes]
rs7954069	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967848	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9737979	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9737985	0.95[AMR][1000 genomes]
rs9738728	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9739233	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv930978	chr12:118866332-119450600	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv899548	chr12:118909907-118987597	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2830233	chr12:118952486-119011469	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1038601	chr12:118958107-119023980	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv523621	chr12:118958608-119019143	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv560391	chr12:118958608-119019143	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1038024	chr12:118965736-119014468	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv541614	chr12:118965736-119014468	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4767685	SLC24A6	cis	parietal	SCAN
rs4767685	PLBD2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118958000-118978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:118970400-118974400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:118970400-118975000	Weak transcription	Ovary	ovary
4	chr12:118970400-118976000	Enhancers	Stomach Smooth Muscle	stomach
5	chr12:118970600-118975600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:118971600-118978600	Weak transcription	Right Atrium	heart
7	chr12:118972400-118975600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:118972800-118975400	Enhancers	Colon Smooth Muscle	Colon
9	chr12:118973000-118974400	Enhancers	Psoas Muscle	Psoas
10	chr12:118973200-118975000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr12:118973200-118976400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr12:118973800-118975200	Enhancers	Placenta	Placenta
13	chr12:118973800-118975400	Enhancers	Aorta	Aorta
14	chr12:118973800-118975600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:118974000-118974600	Enhancers	Fetal Muscle Trunk	muscle
16	chr12:118974000-118975000	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:118974000-118975400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:118974000-118975600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr12:118974000-118975600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr12:118974000-118975600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:118974000-118975600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:118974000-118975800	Enhancers	H9 Cell Line	embryonic stem cell
23	chr12:118974000-118976400	Enhancers	Fetal Heart	heart
24	chr12:118974200-118974400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:118974200-118974400	Enhancers	Right Ventricle	heart
26	chr12:118974200-118974600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr12:118974200-118975400	Enhancers	Left Ventricle	heart
28	chr12:118974200-118975600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:118974200-118975800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:118974200-118976000	Enhancers	NHDF-Ad	bronchial
31	chr12:118974200-118976800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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