Variant report

Variant	rs2850346
Chromosome Location	chr4:102199950-102199951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102199385..102202283-chr4:102207975..102210015,2	MCF-7	breast:
2	chr4:102191153..102193723-chr4:102199346..102202643,3	MCF-7	breast:
3	chr4:102195924..102197828-chr4:102197839..102200644,3	MCF-7	breast:
4	chr4:102198153..102200394-chr4:102259165..102261544,2	MCF-7	breast:
5	chr4:102194719..102197213-chr4:102198296..102200736,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1441429	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17031191	1.00[AFR][1000 genomes]
rs2119599	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119601	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2583388	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583403	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2583404	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850340	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850341	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850342	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850343	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]
rs2850955	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2850956	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850958	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850962	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850965	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850966	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850973	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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:72 , 50 per page) page: 1 2

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	chr4:102188800-102203200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:102191400-102202200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:102191600-102200400	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:102192800-102208600	Weak transcription	Fetal Kidney	kidney
7	chr4:102193000-102203400	Weak transcription	Brain Angular Gyrus	brain
8	chr4:102193800-102201800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:102194000-102205200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:102194200-102203000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:102195400-102200600	Weak transcription	Gastric	stomach
12	chr4:102195400-102203400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:102196600-102200400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr4:102196600-102200400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:102196600-102200400	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:102196600-102200600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:102196600-102200600	Weak transcription	Right Atrium	heart
18	chr4:102196600-102200600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:102196600-102203000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:102196800-102200400	Weak transcription	Primary B cells from cord blood	blood
21	chr4:102196800-102200600	Weak transcription	GM12878-XiMat	blood
22	chr4:102197000-102200400	Weak transcription	HUVEC	blood vessel
23	chr4:102197200-102200800	Weak transcription	Brain Anterior Caudate	brain
24	chr4:102197200-102202200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:102197400-102200400	Weak transcription	Aorta	Aorta
26	chr4:102197400-102203600	Weak transcription	Left Ventricle	heart
27	chr4:102197400-102203600	Weak transcription	Pancreas	Pancrea
28	chr4:102197800-102201400	Enhancers	A549	lung
29	chr4:102198000-102200000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:102198200-102201000	Enhancers	HSMM	muscle
31	chr4:102198400-102200200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:102198400-102201200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:102198400-102201200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:102198400-102201400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:102198400-102206800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:102198600-102200400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:102198600-102201200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr4:102198600-102201400	Enhancers	NH-A	brain
39	chr4:102198600-102201400	Enhancers	Osteobl	bone
40	chr4:102198600-102201600	Enhancers	NHDF-Ad	bronchial
41	chr4:102198600-102203400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:102198800-102200000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:102198800-102200000	Enhancers	HMEC	breast
44	chr4:102198800-102200200	Enhancers	NHEK	skin
45	chr4:102198800-102200400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:102198800-102200800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:102198800-102200800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:102198800-102200800	Weak transcription	HSMMtube	muscle
49	chr4:102198800-102201600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:102198800-102201600	Enhancers	NHLF	lung

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