Variant report

Variant	rs12646021
Chromosome Location	chr4:87276840-87276841
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10213444	0.96[CEU][hapmap]
rs10516773	0.96[CEU][hapmap]
rs12640131	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12641387	0.96[CEU][hapmap]
rs12645370	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13112340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13112497	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13132206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17409311	0.91[CEU][hapmap]
rs17409527	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17409925	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17449485	0.95[CEU][hapmap]
rs17451306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841427	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290881	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28434311	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2869431	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36057902	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6531916	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6531917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826702	0.96[CEU][hapmap]
rs7349681	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7654796	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv934210	chr4:87197339-87325578	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv461574	chr4:87239764-87279096	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv594788	chr4:87239764-87279096	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87260400-87277800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:87260800-87277200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:87264000-87277000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:87264200-87277800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:87264400-87280600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:87265600-87278000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:87266200-87278200	Weak transcription	Fetal Kidney	kidney
8	chr4:87269200-87279400	Weak transcription	Psoas Muscle	Psoas
9	chr4:87269600-87279400	Weak transcription	Ovary	ovary
10	chr4:87270800-87278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:87270800-87279600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:87271200-87277200	Weak transcription	Brain Anterior Caudate	brain
13	chr4:87272200-87280600	Weak transcription	Adipose Nuclei	Adipose
14	chr4:87272600-87280600	Weak transcription	Fetal Lung	lung
15	chr4:87272800-87278000	Weak transcription	Brain Substantia Nigra	brain
16	chr4:87273800-87280600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:87274200-87277800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:87274200-87277800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:87274400-87277200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:87274400-87278200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:87274400-87278800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:87274400-87278800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:87274600-87277200	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:87274600-87277400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:87275400-87279400	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:87275600-87302400	Weak transcription	Aorta	Aorta
27	chr4:87276000-87277600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr4:87276400-87277000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:87276400-87277000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr4:87276400-87277200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:87276400-87277600	Enhancers	Fetal Brain Male	brain
32	chr4:87276400-87281800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:87276600-87277000	Active TSS	Fetal Brain Female	brain
34	chr4:87276800-87277200	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:87276800-87277400	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr4:87276800-87278200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:87276800-87279600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:87276800-87282000	Active TSS	Brain Angular Gyrus	brain

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