Variant report

Variant	rs193196
Chromosome Location	chr3:156506349-156506350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156498434..156501596-chr3:156502537..156507306,7	K562	blood:
2	chr3:156506224..156508447-chr3:156509978..156512261,2	K562	blood:
3	chr3:156497858..156501596-chr3:156502537..156507306,7	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs171079	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2054880	0.84[LWK][hapmap];0.83[MKK][hapmap]
rs34354387	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs343993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs343994	0.83[AFR][1000 genomes]
rs344019	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs344022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344024	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344051	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs386736	0.91[GIH][hapmap]
rs4637242	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6781237	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614210	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs88053	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs193196	C3orf57	cis	parietal	SCAN
rs193196	SSR3	cis	parietal	SCAN
rs193196	IQCJ	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156494600-156510800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:156499000-156507400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:156500200-156508800	Enhancers	HMEC	breast
4	chr3:156500400-156510800	Weak transcription	Stomach Mucosa	stomach
5	chr3:156501000-156510800	Weak transcription	Gastric	stomach
6	chr3:156502000-156506600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:156502200-156507600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:156502400-156510600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:156502600-156510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:156502800-156509000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:156502800-156510800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:156502800-156510800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:156502800-156528400	Weak transcription	Esophagus	oesophagus
14	chr3:156502800-156529000	Weak transcription	Liver	Liver
15	chr3:156503000-156507200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:156504000-156507200	Enhancers	K562	blood
17	chr3:156504000-156507400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:156504000-156509200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:156504200-156508800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:156504200-156516400	Weak transcription	Primary B cells from cord blood	blood
21	chr3:156504600-156507000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:156504800-156508600	Enhancers	HSMM	muscle
23	chr3:156505000-156506600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:156505000-156507000	Enhancers	Hela-S3	cervix
25	chr3:156505000-156507400	Enhancers	NHLF	lung
26	chr3:156505000-156510600	Weak transcription	GM12878-XiMat	blood
27	chr3:156505200-156510600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:156505200-156512400	Weak transcription	Pancreas	Pancrea
29	chr3:156505600-156506600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr3:156505600-156507200	Enhancers	HUVEC	blood vessel
31	chr3:156505600-156507400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:156505600-156507400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:156505800-156506400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:156505800-156506600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:156505800-156506600	Flanking Active TSS	NH-A	brain
36	chr3:156505800-156506600	Flanking Active TSS	Osteobl	bone
37	chr3:156505800-156507400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:156505800-156507400	Flanking Active TSS	A549	lung
39	chr3:156506000-156506400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:156506000-156506400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:156506000-156506400	Enhancers	NHEK	skin
42	chr3:156506000-156507200	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr3:156506000-156507200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:156506200-156506400	Enhancers	Fetal Heart	heart
45	chr3:156506200-156506600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:156506200-156506600	Flanking Active TSS	HSMMtube	muscle
47	chr3:156506200-156506800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:156506200-156506800	Flanking Active TSS	NHDF-Ad	bronchial
49	chr3:156506200-156508400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:156506200-156509400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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