Variant report

Variant	rs838989
Chromosome Location	chr1:120182906-120182907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120177895..120180235-chr1:120180317..120183358,4	K562	blood:
2	chr1:120181739..120184081-chr1:120198210..120201603,3	K562	blood:
3	chr1:120172872..120175188-chr1:120180401..120183308,2	MCF-7	breast:
4	chr1:120178690..120181053-chr1:120181852..120183654,2	MCF-7	breast:
5	chr1:120177198..120184772-chr1:120188907..120196947,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10494228	0.90[JPT][hapmap]
rs10754417	0.90[JPT][hapmap]
rs347904	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs347909	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs347911	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs376910	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];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377033	0.90[JPT][hapmap]
rs454510	0.80[GIH][hapmap];0.90[JPT][hapmap]
rs496886	0.90[JPT][hapmap]
rs838986	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs838987	0.88[EUR][1000 genomes]
rs838990	0.90[JPT][hapmap]

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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120163600-120188400	Weak transcription	Hela-S3	cervix
2	chr1:120165800-120189600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:120168400-120187000	Weak transcription	K562	blood
4	chr1:120169400-120184400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:120174800-120186000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:120175000-120183000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:120175200-120183000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:120175200-120188200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:120175400-120186000	Weak transcription	Aorta	Aorta
10	chr1:120175400-120188000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:120175400-120188200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:120175400-120189200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:120175600-120187800	Weak transcription	HMEC	breast
14	chr1:120175600-120188200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:120175800-120188000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:120176000-120188400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:120176200-120188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:120176800-120184400	Enhancers	Fetal Lung	lung
19	chr1:120176800-120186000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:120177000-120183600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:120177000-120188200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:120177000-120188400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:120177000-120189000	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:120178800-120183800	Enhancers	Fetal Heart	heart
25	chr1:120179000-120188400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:120179000-120188400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:120179200-120184000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:120179400-120184000	Enhancers	HepG2	liver
29	chr1:120179400-120188400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:120179600-120183600	Weak transcription	GM12878-XiMat	blood
31	chr1:120179600-120183800	Enhancers	NHLF	lung
32	chr1:120179600-120187800	Weak transcription	NHEK	skin
33	chr1:120179600-120188000	Weak transcription	NH-A	brain
34	chr1:120179800-120185800	Weak transcription	Osteobl	bone
35	chr1:120180000-120188400	Weak transcription	Fetal Kidney	kidney
36	chr1:120180200-120184200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:120180200-120188400	Weak transcription	Fetal Intestine Small	intestine
38	chr1:120180200-120188600	Weak transcription	Fetal Intestine Large	intestine
39	chr1:120180200-120189000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:120180200-120189200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:120180400-120187200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr1:120180400-120188000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:120180600-120183000	Weak transcription	Brain Germinal Matrix	brain
44	chr1:120180800-120183400	Enhancers	Right Atrium	heart
45	chr1:120181000-120183800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:120181000-120189000	Weak transcription	Fetal Brain Female	brain
47	chr1:120181200-120183800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:120181400-120183400	Enhancers	Left Ventricle	heart
49	chr1:120181400-120183800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:120181600-120183000	Weak transcription	Ovary	ovary

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