Variant report

Variant	rs7627104
Chromosome Location	chr3:116108165-116108166
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12491423	1.00[JPT][hapmap]
rs1541871	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619655	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17646258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs1835674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1920185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1920189	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1920191	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs2116308	0.84[AMR][1000 genomes]
rs2163504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504104	0.93[EUR][1000 genomes]
rs4521220	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785974	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs724115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845203	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs9852860	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs9856796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs988803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877361	chr3:116017931-116138039	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv437338	chr3:116076289-116110635	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2757005	chr3:116085678-116121948	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv2759170	chr3:116085678-116121948	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1014989	chr3:116096198-116109192	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1003543	chr3:116096198-116111430	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3463484	chr3:116098674-116110408	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3463485	chr3:116098674-116110408	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv21066	chr3:116098946-116109977	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv516570	chr3:116099041-116108165	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1011591	chr3:116099041-116109192	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116103000-116142000	Weak transcription	Fetal Lung	lung
2	chr3:116103800-116110600	Weak transcription	Brain Germinal Matrix	brain
3	chr3:116105000-116110200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:116107000-116108200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:116107000-116108600	Enhancers	Brain Cingulate Gyrus	brain
6	chr3:116107000-116109000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:116107000-116109600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:116107200-116108600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr3:116107200-116108600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:116107200-116108600	Enhancers	Brain Hippocampus Middle	brain
11	chr3:116107200-116109800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:116107200-116109800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:116107400-116108400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:116107400-116109200	Enhancers	Colon Smooth Muscle	Colon
15	chr3:116107400-116110000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:116107600-116108200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:116107600-116108200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:116107600-116108200	Enhancers	Brain Anterior Caudate	brain
19	chr3:116107600-116108400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:116107600-116108400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr3:116107600-116108600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:116107600-116108600	Enhancers	Brain Substantia Nigra	brain
23	chr3:116107800-116108200	Enhancers	H9 Cell Line	embryonic stem cell
24	chr3:116107800-116108200	Enhancers	Fetal Stomach	stomach
25	chr3:116107800-116108400	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:116107800-116108600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:116107800-116108600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:116107800-116108600	Enhancers	Fetal Brain Female	brain
29	chr3:116108000-116108400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr3:116108000-116108600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:116108000-116110400	Weak transcription	Fetal Brain Male	brain
32	chr3:116108000-116113400	Weak transcription	Brain Angular Gyrus	brain

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