Variant report

Variant	rs162162
Chromosome Location	chr5:98258933-98258934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98257599..98259877-chr5:98263481..98265627,3	MCF-7	breast:
2	chr5:98258735..98261522-chr5:98261609..98263203,2	MCF-7	breast:
3	chr5:98255571..98257201-chr5:98257380..98259074,2	K562	blood:

Variant related genes	Relation type
ENSG00000153922	Chromatin interaction
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10044680	1.00[EUR][1000 genomes]
rs10045317	1.00[EUR][1000 genomes]
rs10046011	1.00[EUR][1000 genomes]
rs10060286	1.00[EUR][1000 genomes]
rs13358830	1.00[EUR][1000 genomes]
rs1382336	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs161743	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162139	0.84[ASW][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs162141	0.84[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162142	1.00[EUR][1000 genomes]
rs162143	0.84[ASW][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs162157	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162161	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs170579	0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166397	1.00[EUR][1000 genomes]
rs17166450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166454	0.91[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs179175	1.00[EUR][1000 genomes]
rs1828171	1.00[EUR][1000 genomes]
rs28782775	1.00[EUR][1000 genomes]
rs325196	1.00[AMR][1000 genomes]
rs325198	1.00[EUR][1000 genomes]
rs325210	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs325216	1.00[EUR][1000 genomes]
rs327801	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs327802	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs327805	1.00[EUR][1000 genomes]
rs451883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57969582	1.00[EUR][1000 genomes]
rs59156696	1.00[EUR][1000 genomes]
rs61578983	1.00[EUR][1000 genomes]
rs6891520	1.00[EUR][1000 genomes]
rs73151499	1.00[EUR][1000 genomes]
rs73153514	1.00[EUR][1000 genomes]
rs73153532	1.00[EUR][1000 genomes]
rs73155421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73155423	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7727696	0.82[YRI][hapmap];1.00[EUR][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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98200000-98263000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:98215000-98263000	Weak transcription	Esophagus	oesophagus
3	chr5:98228200-98259200	Weak transcription	Spleen	Spleen
4	chr5:98228400-98259200	Weak transcription	Gastric	stomach
5	chr5:98228400-98259400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:98228400-98263000	Weak transcription	Aorta	Aorta
7	chr5:98232000-98259200	Weak transcription	Pancreas	Pancrea
8	chr5:98235000-98262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:98235200-98261600	Weak transcription	Fetal Kidney	kidney
10	chr5:98235400-98262600	Weak transcription	Fetal Brain Male	brain
11	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:98236600-98259000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:98236600-98261000	Weak transcription	Small Intestine	intestine
14	chr5:98236600-98261600	Weak transcription	Fetal Brain Female	brain
15	chr5:98236600-98263000	Weak transcription	Ovary	ovary
16	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
17	chr5:98237000-98259200	Weak transcription	Colonic Mucosa	Colon
18	chr5:98240200-98263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:98240800-98263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:98247400-98259600	Weak transcription	Brain Anterior Caudate	brain
21	chr5:98247400-98262600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:98247600-98262200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:98247600-98262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:98248000-98261600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:98249000-98261400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:98249800-98262000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:98251400-98261000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:98252600-98261200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:98253000-98260200	Strong transcription	K562	blood
30	chr5:98253000-98261800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr5:98253200-98259800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:98253200-98261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:98253200-98263000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:98253400-98261000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:98253600-98260200	Strong transcription	Hela-S3	cervix
36	chr5:98253600-98261200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr5:98253600-98261600	Strong transcription	Fetal Intestine Large	intestine
38	chr5:98253600-98261800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:98253800-98260800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:98253800-98262600	Weak transcription	NHLF	lung
41	chr5:98254000-98261000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:98254000-98261200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:98254000-98262200	Strong transcription	Placenta	Placenta
44	chr5:98254200-98260000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:98254200-98262000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr5:98254400-98259000	Weak transcription	Left Ventricle	heart
47	chr5:98254600-98260400	Strong transcription	A549	lung
48	chr5:98254600-98261200	Strong transcription	Liver	Liver
49	chr5:98254600-98261400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:98254600-98261600	Strong transcription	HMEC	breast

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