Variant report

Variant	rs10877929
Chromosome Location	chr12:40403848-40403849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	12:40402537-40410050..12:40703633-40711447	GM12878	blood:
2	12:40402537-40410050..12:40497414-40501128	K562	blood:
3	12:40402537-40410050..12:40687302-40691796	GM12878	blood:
4	chr12:40401380..40404194-chr12:40458458..40460119,2	K562	blood:
5	12:40402537-40410050..12:40793507-40812339	GM12878	blood:

Variant related genes	Relation type
ENSG00000205592	Chromatin interaction
ENSG00000151229	Chromatin interaction
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10454013	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10506141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10878029	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs11174735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174918	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11174998	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175021	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175027	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175090	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175094	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175106	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11175409	0.87[ASN][1000 genomes]
rs11175456	0.87[ASN][1000 genomes]
rs11564157	0.87[ASN][1000 genomes]
rs11564215	0.84[EUR][1000 genomes]
rs11564279	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs12228213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1542594	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1871895	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2101144	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2128276	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2200085	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2242367	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2708445	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28370636	0.97[EUR][1000 genomes]
rs28370645	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28370647	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28370666	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4533099	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61931530	0.95[EUR][1000 genomes]
rs61933163	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7135815	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301226	0.87[ASN][1000 genomes]
rs7302006	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953143	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7966132	0.81[ASN][1000 genomes]
rs7966741	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967822	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs7973688	0.87[ASN][1000 genomes]
rs7975693	0.85[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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1052202	chr12:40322607-40406760	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40384400-40405200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:40384400-40405400	Weak transcription	Pancreas	Pancrea
3	chr12:40393400-40405400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40394000-40405400	Weak transcription	Left Ventricle	heart
5	chr12:40394000-40410800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:40394400-40405000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:40394400-40405200	Weak transcription	Hela-S3	cervix
8	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:40395200-40405400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:40403800-40404200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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