Variant report

Variant	rs11171923
Chromosome Location	chr12:39777633-39777634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39774786..39777930-chr12:39781565..39783444,3	K562	blood:
2	chr12:39775530..39777936-chr12:39825264..39827786,2	K562	blood:
3	chr12:39772032..39774907-chr12:39777578..39779495,2	K562	blood:
4	chr12:39775693..39777906-chr12:39834748..39837680,3	K562	blood:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10876868	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876876	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876972	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11171674	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171675	0.83[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171676	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171720	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11171730	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11171789	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171891	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171901	0.86[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171938	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11172108	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs11172120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11172183	0.82[CEU][hapmap];0.94[JPT][hapmap]
rs11172282	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs11172492	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11172592	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs11172661	0.87[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs11830643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11836755	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12228767	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230604	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12424345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512942	0.85[ASN][1000 genomes]
rs1567739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127019	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1828653	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1955314	0.80[ASN][1000 genomes]
rs2388320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736466	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4284427	0.91[CEU][hapmap];0.93[JPT][hapmap]
rs4320988	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4492858	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4500523	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs57756176	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57833783	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58240943	0.84[ASN][1000 genomes]
rs58613501	0.83[ASN][1000 genomes]
rs60792848	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7137143	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73094410	0.83[ASN][1000 genomes]
rs7316073	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs7953548	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7962283	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs7964447	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965222	0.82[ASN][1000 genomes]
rs7968837	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7971515	0.87[ASN][1000 genomes]
rs7974928	0.84[CEU][hapmap]
rs7979329	0.87[ASN][1000 genomes]
rs7979444	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs958914	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
2	chr12:39745000-39778600	Weak transcription	Pancreas	Pancrea
3	chr12:39757000-39784600	Weak transcription	Brain Germinal Matrix	brain
4	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
5	chr12:39763000-39781400	Weak transcription	A549	lung
6	chr12:39764000-39781000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:39767400-39784800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:39767600-39791400	Weak transcription	GM12878-XiMat	blood
9	chr12:39767800-39784800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:39772200-39778600	Weak transcription	Brain Anterior Caudate	brain
11	chr12:39772200-39778800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:39772400-39780200	Weak transcription	Brain Substantia Nigra	brain
13	chr12:39772600-39778200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:39772600-39778400	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:39772800-39778200	Weak transcription	Brain Angular Gyrus	brain
16	chr12:39772800-39778400	Weak transcription	Fetal Heart	heart
17	chr12:39776400-39783200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:39776600-39783800	Weak transcription	HMEC	breast
19	chr12:39777000-39783200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:39777400-39778800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:39777400-39779000	Enhancers	Right Atrium	heart
22	chr12:39777600-39778000	Weak transcription	Left Ventricle	heart
23	chr12:39777600-39778600	Weak transcription	Psoas Muscle	Psoas
24	chr12:39777600-39778800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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