Variant report

Variant	rs4047189
Chromosome Location	chr2:234442949-234442950
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234436536..234438421-chr2:234442924..234444857,2	MCF-7	breast:
2	chr2:234442059..234444309-chr2:234445445..234448239,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10929178	0.85[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11675858	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676524	1.00[ASW][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11686188	0.83[ASW][hapmap];0.85[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796090	0.89[JPT][hapmap]
rs3796092	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6704644	0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6746234	0.91[ASW][hapmap];0.85[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72980395	0.80[EUR][1000 genomes]
rs72980402	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72982309	0.86[EUR][1000 genomes]
rs72982316	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72982325	0.89[AMR][1000 genomes];0.91[EUR][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4047189	SP110	cis	parietal	SCAN
rs4047189	ECEL1P2	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr2:234398000-234452800	Weak transcription	HUVEC	blood vessel
3	chr2:234402200-234472400	Weak transcription	Psoas Muscle	Psoas
4	chr2:234402600-234454000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:234404400-234455000	Weak transcription	Fetal Thymus	thymus
6	chr2:234411600-234465600	Weak transcription	Thymus	Thymus
7	chr2:234413000-234474200	Weak transcription	Fetal Heart	heart
8	chr2:234414000-234461800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:234423200-234473400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:234426200-234474000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:234426400-234453600	Weak transcription	NH-A	brain
12	chr2:234427000-234466200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:234427400-234463800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:234428800-234474400	Weak transcription	Brain Germinal Matrix	brain
15	chr2:234430200-234473800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:234430400-234443600	Weak transcription	GM12878-XiMat	blood
17	chr2:234430400-234453800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:234430800-234472800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:234431600-234452200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:234432000-234467600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:234432200-234443200	Weak transcription	NHDF-Ad	bronchial
22	chr2:234432200-234444000	Weak transcription	HMEC	breast
23	chr2:234432200-234447400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:234432200-234452000	Weak transcription	Small Intestine	intestine
25	chr2:234432200-234453000	Weak transcription	Fetal Lung	lung
26	chr2:234432200-234454000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:234432200-234474800	Weak transcription	Spleen	Spleen
28	chr2:234432600-234474400	Weak transcription	Colonic Mucosa	Colon
29	chr2:234432800-234445400	Weak transcription	Pancreas	Pancrea
30	chr2:234432800-234453600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:234433000-234462600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:234434600-234454000	Weak transcription	Brain Substantia Nigra	brain
33	chr2:234434600-234466200	Weak transcription	Right Ventricle	heart
34	chr2:234437200-234474400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:234437800-234453800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:234438000-234459800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:234438200-234447400	Weak transcription	Ovary	ovary
38	chr2:234438400-234447400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:234439000-234443200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:234440000-234444000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:234440200-234458200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:234440400-234443600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:234440400-234443800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:234440400-234444000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:234440400-234446200	Strong transcription	Liver	Liver
46	chr2:234440400-234450400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:234440600-234443000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:234440600-234443000	Strong transcription	Placenta	Placenta
49	chr2:234440600-234443000	Strong transcription	NHEK	skin
50	chr2:234440600-234443800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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