Variant report

Variant	rs2850965
Chromosome Location	chr4:102178963-102178964
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102178495..102180212-chr4:102267850..102269476,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138814	Chromatin interaction
ENSG00000254531	Chromatin interaction

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];0.98[EUR][1000 genomes];0.97[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];1.00[EUR][1000 genomes];0.95[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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2583388	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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];0.95[ASN][1000 genomes]
rs2583404	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850342	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850343	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]
rs2850346	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]
rs2850950	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[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];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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];1.00[EUR][1000 genomes];0.95[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];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];1.00[EUR][1000 genomes];0.97[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];1.00[EUR][1000 genomes];0.97[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];1.00[EUR][1000 genomes];0.97[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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102157800-102179600	Weak transcription	Primary B cells from cord blood	blood
2	chr4:102159200-102179800	Weak transcription	Psoas Muscle	Psoas
3	chr4:102166200-102179400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:102173200-102179400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:102174000-102181200	Weak transcription	Brain Anterior Caudate	brain
6	chr4:102174200-102179400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:102174200-102179600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:102174200-102179800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:102174200-102180000	Weak transcription	Left Ventricle	heart
10	chr4:102174200-102181000	Weak transcription	Adipose Nuclei	Adipose
11	chr4:102174200-102186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:102174400-102180000	Weak transcription	NHDF-Ad	bronchial
13	chr4:102174400-102180600	Weak transcription	NHLF	lung
14	chr4:102174400-102185800	Weak transcription	HMEC	breast
15	chr4:102174600-102179800	Weak transcription	Ovary	ovary
16	chr4:102175200-102180000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:102175400-102179800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:102175800-102179000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr4:102175800-102180400	Weak transcription	NH-A	brain
20	chr4:102176000-102179600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:102176200-102181000	Weak transcription	Fetal Kidney	kidney
22	chr4:102176400-102180400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:102176600-102179800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr4:102177800-102179000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:102177800-102179400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:102177800-102180200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:102177800-102181000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:102177800-102181600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:102177800-102185000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:102178000-102179000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:102178000-102179200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:102178000-102179600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:102178000-102179600	Weak transcription	A549	lung
34	chr4:102178000-102179800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:102178000-102179800	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:102178000-102179800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:102178000-102181800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:102178000-102186600	Weak transcription	Brain Substantia Nigra	brain
39	chr4:102178200-102179400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:102178200-102179400	Weak transcription	Small Intestine	intestine
41	chr4:102178200-102179600	Weak transcription	HUVEC	blood vessel
42	chr4:102178200-102180000	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:102178200-102182200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:102178200-102183000	Weak transcription	Stomach Mucosa	stomach
45	chr4:102178200-102183800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:102178800-102179000	Enhancers	Primary T helper cells PMA-I stimulated	--

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