Variant report

Variant	rs12630004
Chromosome Location	chr3:156034438-156034439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1027530	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs10513486	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12629802	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1375925	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1375926	0.93[CHB][hapmap]
rs1874952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2122419	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs2167143	0.92[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28413487	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3755625	0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs3755627	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs3772231	0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3772233	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3772236	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772243	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821415	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4680258	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680259	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6795493	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7653024	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882089	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs9874261	0.94[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv877682	chr3:156019961-156077514	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156021400-156035200	Weak transcription	Stomach Mucosa	stomach
2	chr3:156021800-156035800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:156022800-156035600	Weak transcription	Brain Anterior Caudate	brain
4	chr3:156026400-156038400	Weak transcription	Aorta	Aorta
5	chr3:156029800-156035000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:156030000-156035000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:156030000-156035200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:156030000-156035400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:156030000-156035400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:156030000-156035400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:156030200-156034800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:156030600-156036400	Enhancers	Hela-S3	cervix
13	chr3:156030800-156035600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:156032000-156035000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:156032000-156035200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:156033200-156034600	Weak transcription	HMEC	breast
17	chr3:156033200-156034600	Weak transcription	NHEK	skin
18	chr3:156033200-156037000	Weak transcription	Left Ventricle	heart
19	chr3:156034000-156036000	Enhancers	Rectal Smooth Muscle	rectum
20	chr3:156034000-156036600	Enhancers	HUVEC	blood vessel
21	chr3:156034400-156035000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:156034400-156035800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:156034400-156036000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:156034400-156036200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:156034400-156036200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:156034400-156036400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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