Variant report

Variant	rs1872296
Chromosome Location	chr4:143231657-143231658
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10013303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10024947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025044	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11945996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16998530	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17015920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34991177	0.82[ASN][1000 genomes]
rs35157240	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35298298	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62328283	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62328284	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62328285	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62328295	0.85[ASN][1000 genomes]
rs6811427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6816219	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6817826	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6847957	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6850050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6858661	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs960680	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9654253	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143200000-143240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:143204600-143233600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:143206000-143233400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:143210800-143235400	Weak transcription	Right Ventricle	heart
5	chr4:143215200-143235200	Weak transcription	Osteobl	bone
6	chr4:143215800-143235200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:143216200-143234600	Weak transcription	Thymus	Thymus
8	chr4:143216600-143233600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:143217600-143238600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:143217600-143260800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:143218200-143233400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:143218800-143234600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:143219200-143233600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:143219400-143232600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:143219400-143236600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:143220600-143233000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:143221600-143234800	Weak transcription	Pancreas	Pancrea
18	chr4:143221800-143233000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:143222600-143233800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr4:143223600-143239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:143224400-143234800	Strong transcription	Dnd41	blood
22	chr4:143225200-143235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:143225400-143237400	Weak transcription	Ovary	ovary
24	chr4:143225400-143240200	Weak transcription	Esophagus	oesophagus
25	chr4:143225800-143233200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:143225800-143234600	Weak transcription	NHDF-Ad	bronchial
27	chr4:143227200-143233200	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:143227400-143233800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:143228000-143233800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:143228600-143232000	Weak transcription	HMEC	breast
31	chr4:143228800-143234600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:143229000-143235600	Strong transcription	NHEK	skin
33	chr4:143229200-143232600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:143229200-143233600	Weak transcription	Aorta	Aorta
35	chr4:143229200-143233800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:143229400-143232200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:143229400-143232800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:143229400-143234600	Weak transcription	Small Intestine	intestine
39	chr4:143229400-143235600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:143229600-143232600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:143229600-143234600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:143230200-143233400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:143230600-143232000	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr4:143231000-143232200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:143231000-143235000	Weak transcription	Fetal Intestine Small	intestine
46	chr4:143231200-143231800	Weak transcription	HSMM	muscle
47	chr4:143231200-143232000	Weak transcription	Primary T cells from cord blood	blood
48	chr4:143231200-143232000	Weak transcription	Right Atrium	heart
49	chr4:143231200-143232200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr4:143231200-143233200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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