Variant report

Variant	rs28365683
Chromosome Location	chr12:40446291-40446292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	12:40441273-40454218..12:40703633-40711447	GM12878	blood:
2	chr12:40445246..40446962-chr12:40448695..40451443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10082797	0.82[CHB][hapmap]
rs10784340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878036	0.81[CHB][hapmap]
rs10878123	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11174603	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11174831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174928	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175102	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175103	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175256	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11175260	0.86[EUR][1000 genomes]
rs11175401	1.00[CEU][hapmap]
rs11175422	1.00[CEU][hapmap]
rs12372213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581285	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1491924	1.00[CEU][hapmap]
rs17442157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17458156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17458613	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17518546	0.86[EUR][1000 genomes]
rs28365172	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28365179	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28370683	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971218	0.82[CHB][hapmap]
rs949640	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
3	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
4	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:40442200-40447600	Weak transcription	A549	lung
7	chr12:40442200-40451400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:40444000-40453400	Weak transcription	Right Ventricle	heart
9	chr12:40444400-40447600	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:40445000-40448400	Weak transcription	Fetal Stomach	stomach
11	chr12:40445000-40448600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:40446000-40446600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:40446000-40446600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr12:40446200-40446600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:40446200-40446600	Enhancers	H1 Cell Line	embryonic stem cell

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