Variant report

Variant	rs2850343
Chromosome Location	chr4:102197855-102197856
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	chr4:102195924..102197828-chr4:102197839..102200644,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1441429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17031191	1.00[ASW][hapmap]
rs2119599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2119601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583404	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850340	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850342	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850346	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850950	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.87[AFR][1000 genomes]
rs2850952	0.87[AFR][1000 genomes]
rs2850955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2850956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850966	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850973	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102180600-102203000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:102184000-102203200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:102184400-102199600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:102184600-102199400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:102188800-102203200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:102191400-102202200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:102191600-102200400	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:102192800-102208600	Weak transcription	Fetal Kidney	kidney
9	chr4:102193000-102198800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:102193000-102198800	Weak transcription	Small Intestine	intestine
11	chr4:102193000-102199600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:102193000-102203400	Weak transcription	Brain Angular Gyrus	brain
13	chr4:102193600-102198400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:102193800-102198400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:102193800-102199600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:102193800-102201800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:102194000-102205200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:102194200-102203000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:102195400-102199400	Weak transcription	Psoas Muscle	Psoas
20	chr4:102195400-102200600	Weak transcription	Gastric	stomach
21	chr4:102195400-102203400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:102196600-102198400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:102196600-102198600	Weak transcription	HSMMtube	muscle
24	chr4:102196600-102198800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:102196600-102200400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:102196600-102200400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:102196600-102200400	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:102196600-102200600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:102196600-102200600	Weak transcription	Right Atrium	heart
30	chr4:102196600-102200600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr4:102196600-102203000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:102196800-102198400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:102196800-102198600	Weak transcription	NH-A	brain
34	chr4:102196800-102199600	Weak transcription	HepG2	liver
35	chr4:102196800-102200400	Weak transcription	Primary B cells from cord blood	blood
36	chr4:102196800-102200600	Weak transcription	GM12878-XiMat	blood
37	chr4:102197000-102198600	Weak transcription	Osteobl	bone
38	chr4:102197000-102200400	Weak transcription	HUVEC	blood vessel
39	chr4:102197200-102199600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr4:102197200-102200800	Weak transcription	Brain Anterior Caudate	brain
41	chr4:102197200-102202200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:102197400-102198800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:102197400-102199800	Weak transcription	Ovary	ovary
44	chr4:102197400-102200400	Weak transcription	Aorta	Aorta
45	chr4:102197400-102203600	Weak transcription	Left Ventricle	heart
46	chr4:102197400-102203600	Weak transcription	Pancreas	Pancrea
47	chr4:102197800-102198200	Weak transcription	Fetal Stomach	stomach
48	chr4:102197800-102201400	Enhancers	A549	lung

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