Variant report

Variant	rs11945996
Chromosome Location	chr4:143235721-143235722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:143235350-143235727	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
LSM3P4	TF binding region

Extended variants
information (count: 29 )
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];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10024947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10025044	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10034842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1872296	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]
rs34991177	0.85[ASN][1000 genomes]
rs35157240	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35298298	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328283	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62328284	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328285	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328295	0.89[ASN][1000 genomes]
rs6811427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6812034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6816219	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6817826	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6847957	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858661	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs960680	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9654253	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];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	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	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
4	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	chr4:143217600-143238600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:143217600-143260800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:143219400-143236600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:143223600-143239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:143225200-143235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:143225400-143237400	Weak transcription	Ovary	ovary
8	chr4:143225400-143240200	Weak transcription	Esophagus	oesophagus
9	chr4:143231400-143239400	Weak transcription	HSMMtube	muscle
10	chr4:143232000-143236200	Strong transcription	HMEC	breast
11	chr4:143232400-143236200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:143232800-143236200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:143233000-143236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr4:143233600-143236200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:143233800-143236200	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr4:143233800-143241000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:143233800-143257200	Weak transcription	Left Ventricle	heart
18	chr4:143234000-143236000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr4:143234000-143236000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:143234000-143236200	Enhancers	Fetal Thymus	thymus
21	chr4:143234000-143236400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:143234000-143242000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:143234200-143235800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr4:143234200-143236000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr4:143234200-143240000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:143234400-143236200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:143234600-143235800	Enhancers	Fetal Heart	heart
28	chr4:143234600-143236000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr4:143234600-143236000	Enhancers	Thymus	Thymus
30	chr4:143234600-143236200	Enhancers	Primary hematopoietic stem cells	blood
31	chr4:143234600-143237400	Enhancers	Small Intestine	intestine
32	chr4:143234600-143237600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:143234800-143236000	Enhancers	Fetal Muscle Leg	muscle
34	chr4:143234800-143236400	Genic enhancers	Dnd41	blood
35	chr4:143234800-143236600	Enhancers	Stomach Mucosa	stomach
36	chr4:143234800-143271800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:143235000-143236000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr4:143235000-143236400	Enhancers	Fetal Intestine Small	intestine
39	chr4:143235000-143237400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:143235000-143240000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:143235000-143240200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr4:143235000-143243200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:143235000-143244200	Weak transcription	NHDF-Ad	bronchial
44	chr4:143235200-143236000	Active TSS	Colonic Mucosa	Colon
45	chr4:143235400-143235800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:143235400-143235800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:143235400-143235800	Genic enhancers	HSMM	muscle
48	chr4:143235400-143236000	Enhancers	Gastric	stomach
49	chr4:143235400-143236000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr4:143235400-143236200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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