Variant report

Variant	rs2850968
Chromosome Location	chr4:102182209-102182210
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	chr4:102176705..102178742-chr4:102180562..102183503,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1441429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2119601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583388	1.00[AMR][1000 genomes];0.97[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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583404	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850342	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850343	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]
rs2850346	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]
rs2850950	0.87[AFR][1000 genomes]
rs2850952	0.87[AFR][1000 genomes]
rs2850955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2850956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850966	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102174200-102186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:102174400-102185800	Weak transcription	HMEC	breast
3	chr4:102177800-102185000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr4:102178000-102186600	Weak transcription	Brain Substantia Nigra	brain
5	chr4:102178200-102183000	Weak transcription	Stomach Mucosa	stomach
6	chr4:102178200-102183800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:102179000-102186800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:102179600-102182400	Enhancers	A549	lung
9	chr4:102179800-102182600	Enhancers	Colon Smooth Muscle	Colon
10	chr4:102180200-102185800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:102180400-102183800	Weak transcription	Small Intestine	intestine
12	chr4:102180600-102183800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:102180600-102185400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:102180600-102185800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:102180600-102186200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:102180600-102186200	Weak transcription	Pancreas	Pancrea
17	chr4:102180600-102191000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:102180600-102192400	Weak transcription	Ovary	ovary
19	chr4:102180600-102197000	Weak transcription	Left Ventricle	heart
20	chr4:102180600-102203000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:102180800-102182600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:102180800-102186200	Weak transcription	Gastric	stomach
23	chr4:102181000-102182600	Enhancers	Adipose Nuclei	Adipose
24	chr4:102181000-102182600	Enhancers	Fetal Kidney	kidney
25	chr4:102181200-102183800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:102181200-102183800	Weak transcription	Psoas Muscle	Psoas
27	chr4:102181200-102183800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:102181200-102184000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:102181200-102185800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:102181200-102186600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:102181200-102186800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr4:102181400-102182400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr4:102181400-102182800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr4:102181400-102183200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:102181400-102184000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:102181400-102186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:102181600-102182400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:102181600-102183800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:102181600-102185000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr4:102181800-102182400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:102181800-102182600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr4:102181800-102183000	Weak transcription	Primary B cells from cord blood	blood
43	chr4:102181800-102184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:102181800-102185600	Weak transcription	NH-A	brain
45	chr4:102182000-102182400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:102182000-102182600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:102182000-102185000	Weak transcription	HUVEC	blood vessel
48	chr4:102182000-102185200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:102182200-102182400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:102182200-102182400	Enhancers	Fetal Heart	heart

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