Variant report

Variant	rs6539201
Chromosome Location	chr12:105673988-105673989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10778371	0.84[CHB][hapmap]
rs4964130	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964344	0.81[ASN][1000 genomes]
rs4964345	0.81[ASN][1000 genomes]
rs4964348	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4964350	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964353	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs6419391	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66925241	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7134360	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71441894	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7300300	0.81[ASN][1000 genomes]
rs7358662	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959327	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7970588	0.86[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970719	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978648	0.91[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1044450	chr12:105668451-105682822	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105665000-105674200	Weak transcription	Osteobl	bone
2	chr12:105665600-105674800	Weak transcription	NHDF-Ad	bronchial
3	chr12:105668200-105674800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:105670400-105674600	Weak transcription	NHEK	skin
5	chr12:105670400-105674800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:105670600-105675000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:105670600-105675000	Weak transcription	HMEC	breast
8	chr12:105672800-105674200	Weak transcription	Fetal Intestine Small	intestine
9	chr12:105673000-105674000	Enhancers	A549	lung
10	chr12:105673200-105674000	Weak transcription	Fetal Intestine Large	intestine
11	chr12:105673200-105675800	Enhancers	Stomach Mucosa	stomach
12	chr12:105673200-105676200	Enhancers	HepG2	liver
13	chr12:105673400-105674200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:105673400-105674200	Enhancers	Gastric	stomach
15	chr12:105673400-105674200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr12:105673400-105674400	Enhancers	Pancreas	Pancrea
17	chr12:105673800-105674800	Weak transcription	Rectal Mucosa Donor 31	rectum

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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