Variant report

Variant	rs9995896
Chromosome Location	chr4:148746300-148746301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148738987..148741967-chr4:148743757..148746836,3	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10003507	0.82[CEU][hapmap]
rs10004138	0.82[CEU][hapmap]
rs10004792	0.82[CEU][hapmap]
rs10004850	0.99[ASN][1000 genomes]
rs10005192	0.85[CEU][hapmap]
rs10007231	0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10014696	0.82[CEU][hapmap]
rs10018820	0.82[CEU][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10018903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10021936	0.92[ASN][1000 genomes]
rs10022691	0.93[ASN][1000 genomes]
rs10025684	0.95[ASN][1000 genomes]
rs10026985	0.82[CEU][hapmap]
rs10029385	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10030358	0.82[CEU][hapmap]
rs10030513	0.95[ASN][1000 genomes]
rs10049932	0.82[CEU][hapmap]
rs10461235	0.86[CHB][hapmap]
rs10519917	0.85[CEU][hapmap]
rs11099671	0.82[CEU][hapmap]
rs11099672	0.82[CEU][hapmap]
rs11724795	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes]
rs11735412	0.82[CEU][hapmap]
rs11935450	0.85[CEU][hapmap]
rs11935510	0.85[CEU][hapmap]
rs11935620	0.85[CEU][hapmap]
rs11940379	0.82[CEU][hapmap]
rs12331562	0.82[CEU][hapmap]
rs12509618	0.82[CEU][hapmap]
rs12513192	0.82[CEU][hapmap]
rs12641291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12647314	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12650219	1.00[CEU][hapmap]
rs13116821	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13129325	0.82[CEU][hapmap]
rs13129747	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13434396	0.93[ASN][1000 genomes]
rs1347596	0.81[ASN][1000 genomes]
rs1369958	0.82[CEU][hapmap]
rs1436489	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1436490	0.96[ASN][1000 genomes]
rs17023870	0.85[CEU][hapmap]
rs17023919	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17023928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17023995	0.93[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs17024037	0.82[CEU][hapmap]
rs17613979	0.82[CEU][hapmap]
rs17614025	0.82[CEU][hapmap]
rs17676080	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs2043644	1.00[CEU][hapmap]
rs28662484	0.94[ASN][1000 genomes]
rs35115631	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3893175	0.82[CEU][hapmap]
rs3990920	0.82[CEU][hapmap]
rs4240338	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4240339	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240341	0.82[CEU][hapmap]
rs4419463	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4491995	0.82[CEU][hapmap]
rs4571312	0.82[CEU][hapmap]
rs4835461	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs62330695	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66488204	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6818371	0.82[CEU][hapmap]
rs6839440	0.88[ASN][1000 genomes]
rs6840771	0.82[CEU][hapmap]
rs6843392	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs6856273	0.82[CEU][hapmap]
rs7655236	0.85[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7660508	0.82[CEU][hapmap]
rs7666127	0.82[CEU][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs893022	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs893033	0.82[CEU][hapmap]
rs9991741	0.82[CEU][hapmap]
rs9994650	0.82[CEU][hapmap]
rs9995956	0.82[CEU][hapmap]
rs9996108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996209	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9997027	0.82[CEU][hapmap]

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	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148734600-148761000	Weak transcription	Fetal Kidney	kidney
2	chr4:148737000-148747200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:148737200-148758200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:148737600-148746800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:148737600-148747000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:148737600-148747000	Weak transcription	Gastric	stomach
7	chr4:148737600-148750400	Weak transcription	Lung	lung
8	chr4:148737600-148751000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:148737800-148751400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:148737800-148755400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:148737800-148757000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:148737800-148782200	Weak transcription	Thymus	Thymus
13	chr4:148738600-148750400	Weak transcription	Placenta	Placenta
14	chr4:148741400-148754000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:148742200-148746600	Enhancers	Pancreas	Pancrea
16	chr4:148742600-148747000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:148742600-148747400	Weak transcription	Spleen	Spleen
18	chr4:148742600-148751000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:148743000-148746800	Weak transcription	NH-A	brain
20	chr4:148743000-148750400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:148743200-148782200	Weak transcription	Fetal Intestine Large	intestine
22	chr4:148743400-148747000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:148743400-148749400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:148743600-148746600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:148743600-148746800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:148743600-148746800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:148743600-148746800	Weak transcription	HUVEC	blood vessel
28	chr4:148743600-148746800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr4:148743600-148750600	Weak transcription	Fetal Lung	lung
30	chr4:148743600-148752000	Weak transcription	Brain Anterior Caudate	brain
31	chr4:148743600-148752200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:148743600-148755400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:148743800-148746800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:148743800-148750400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:148743800-148750600	Weak transcription	Small Intestine	intestine
36	chr4:148743800-148750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:148743800-148751000	Weak transcription	Fetal Thymus	thymus
38	chr4:148744000-148747000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:148744000-148747000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:148744000-148747000	Weak transcription	NHLF	lung
41	chr4:148744000-148747200	Enhancers	HMEC	breast
42	chr4:148744200-148746400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:148744200-148747000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:148744200-148747800	Strong transcription	Fetal Stomach	stomach
45	chr4:148744400-148746600	Weak transcription	Adipose Nuclei	Adipose
46	chr4:148744400-148746800	Weak transcription	Stomach Mucosa	stomach
47	chr4:148744400-148748000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:148744400-148750600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:148744600-148746400	Strong transcription	Fetal Intestine Small	intestine
50	chr4:148744600-148746600	Weak transcription	Fetal Heart	heart

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