Variant report

Variant	rs12121447
Chromosome Location	chr1:120216971-120216972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120216915..120218562-chr1:120252926..120255494,2	MCF-7	breast:
2	chr1:120207222..120209789-chr1:120216328..120218570,3	K562	blood:
3	chr1:120204131..120206731-chr1:120214943..120217556,2	MCF-7	breast:
4	chr1:120215638..120218365-chr1:120219886..120221935,2	K562	blood:
5	chr1:120216865..120219033-chr1:120220435..120223044,2	K562	blood:
6	chr1:120189265..120193710-chr1:120213010..120218911,11	MCF-7	breast:
7	chr1:120189180..120192171-chr1:120215646..120218336,2	K562	blood:
8	chr1:120215935..120218673-chr1:120225082..120226675,2	MCF-7	breast:
9	chr1:120216390..120222237-chr1:120252306..120257638,5	MCF-7	breast:
10	chr1:120216874..120219563-chr1:120253751..120255810,3	K562	blood:
11	chr1:120171369..120174303-chr1:120214777..120217221,2	K562	blood:
12	chr1:120189291..120191976-chr1:120215677..120217877,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10494229	0.81[TSI][hapmap]
rs10802125	1.00[ASN][1000 genomes]
rs10923868	1.00[ASN][1000 genomes]
rs10923870	1.00[ASN][1000 genomes]
rs11577560	0.81[TSI][hapmap]
rs11586489	1.00[ASN][1000 genomes]
rs12032931	1.00[CHB][hapmap]
rs12119140	1.00[ASN][1000 genomes]
rs12127605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129705	1.00[ASN][1000 genomes]
rs12139088	1.00[ASN][1000 genomes]
rs12144094	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17258348	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1853048	0.81[CEU][hapmap]
rs34662109	1.00[ASN][1000 genomes]
rs35821663	1.00[ASN][1000 genomes]
rs3850870	1.00[CHB][hapmap]
rs4077553	1.00[ASN][1000 genomes]
rs4481896	1.00[ASN][1000 genomes]
rs4659210	1.00[ASN][1000 genomes]
rs56051540	1.00[ASN][1000 genomes]
rs56096705	1.00[ASN][1000 genomes]
rs6672394	1.00[CHB][hapmap]
rs72695107	1.00[ASN][1000 genomes]
rs72695109	1.00[ASN][1000 genomes]
rs72695117	1.00[ASN][1000 genomes]
rs72695123	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS 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 miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12121447	HSD3B2	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120203800-120217800	Weak transcription	Fetal Stomach	stomach
2	chr1:120210200-120218000	Weak transcription	GM12878-XiMat	blood
3	chr1:120212800-120218000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:120214800-120218000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:120215000-120217800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:120215200-120217400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:120215200-120217600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:120215200-120218000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:120215200-120219000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:120215200-120219600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:120215400-120217200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:120215400-120217800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:120215400-120217800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:120215400-120218000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:120215800-120217400	Enhancers	Ovary	ovary
16	chr1:120215800-120218000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:120216000-120217000	Enhancers	HepG2	liver
18	chr1:120216000-120217000	Enhancers	NHLF	lung
19	chr1:120216000-120217200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:120216000-120217200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr1:120216000-120217200	Enhancers	Fetal Kidney	kidney
22	chr1:120216000-120217600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr1:120216000-120217600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:120216000-120217600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:120216000-120218000	Enhancers	HSMMtube	muscle
26	chr1:120216000-120218000	Enhancers	NH-A	brain
27	chr1:120216200-120217200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:120216200-120217400	Weak transcription	Stomach Mucosa	stomach
29	chr1:120216200-120217800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:120216200-120218000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:120216200-120218600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:120216400-120217200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:120216400-120217800	Enhancers	Liver	Liver
34	chr1:120216400-120218000	Weak transcription	Fetal Intestine Small	intestine
35	chr1:120216400-120218000	Enhancers	NHDF-Ad	bronchial
36	chr1:120216600-120217000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:120216600-120217200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:120216600-120217400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:120216600-120217400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:120216600-120217400	Flanking Active TSS	HMEC	breast
41	chr1:120216600-120217600	Flanking Active TSS	Osteobl	bone
42	chr1:120216600-120217800	Enhancers	Fetal Heart	heart
43	chr1:120216600-120217800	Enhancers	Fetal Lung	lung
44	chr1:120216600-120218000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:120216600-120218000	Enhancers	HSMM	muscle
46	chr1:120216600-120218000	Enhancers	K562	blood
47	chr1:120216600-120218400	Flanking Active TSS	NHEK	skin
48	chr1:120216600-120218600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr1:120216600-120218800	Flanking Active TSS	HUVEC	blood vessel
50	chr1:120216800-120217000	Enhancers	HUES6 Cell Line	embryonic stem cell

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