Variant report

Variant	rs838986
Chromosome Location	chr1:120175121-120175122
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120169996..120174289-chr1:120174706..120179786,6	MCF-7	breast:
2	chr1:120162086..120165079-chr1:120173514..120175556,2	MCF-7	breast:
3	chr1:120174871..120178397-chr1:120178450..120180303,3	K562	blood:
4	chr1:120172872..120175188-chr1:120180401..120183308,2	MCF-7	breast:
5	chr1:120174001..120176369-chr1:120189431..120193664,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10494228	0.90[JPT][hapmap]
rs10754417	0.90[JPT][hapmap]
rs347904	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs347909	0.88[EUR][1000 genomes]
rs347911	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs376910	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs377033	0.90[JPT][hapmap]
rs431441	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs454510	0.90[JPT][hapmap]
rs496886	0.90[JPT][hapmap]
rs7531516	0.86[ASN][1000 genomes]
rs838987	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838989	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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:96 , 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	chr1:120168800-120175800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:120169000-120178400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:120169400-120178400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:120169400-120184400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:120172800-120177400	Enhancers	Fetal Kidney	kidney
9	chr1:120173200-120175400	Enhancers	Placenta	Placenta
10	chr1:120173400-120175400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:120173400-120175400	Enhancers	Lung	lung
12	chr1:120173600-120175200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:120173600-120175200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr1:120173600-120175200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr1:120173600-120175400	Enhancers	Spleen	Spleen
16	chr1:120173600-120175600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:120173600-120175600	Enhancers	HMEC	breast
18	chr1:120173800-120175200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:120173800-120175200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
20	chr1:120173800-120175400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:120173800-120175400	Enhancers	Gastric	stomach
22	chr1:120173800-120175600	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:120173800-120175800	Flanking Active TSS	HUVEC	blood vessel
24	chr1:120174000-120175200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:120174400-120175200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:120174400-120175400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:120174400-120175400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:120174400-120175400	Bivalent Enhancer	Fetal Thymus	thymus
29	chr1:120174400-120175400	Bivalent Enhancer	Stomach Mucosa	stomach
30	chr1:120174400-120175600	Enhancers	NH-A	brain
31	chr1:120174400-120176200	Flanking Active TSS	Fetal Heart	heart
32	chr1:120174400-120176600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:120174600-120175200	Enhancers	H9 Cell Line	embryonic stem cell
34	chr1:120174600-120175200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr1:120174600-120175200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr1:120174600-120175200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:120174600-120175200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:120174600-120175200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr1:120174600-120175200	Enhancers	Colonic Mucosa	Colon
40	chr1:120174600-120175200	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:120174600-120175200	Flanking Active TSS	HepG2	liver
42	chr1:120174600-120175200	Flanking Active TSS	Osteobl	bone
43	chr1:120174600-120175400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:120174600-120175400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:120174600-120175400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:120174600-120175400	Enhancers	Aorta	Aorta
47	chr1:120174600-120175400	Enhancers	Brain Germinal Matrix	brain
48	chr1:120174600-120175400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:120174600-120175400	Enhancers	Fetal Brain Female	brain
50	chr1:120174600-120175400	Enhancers	Fetal Intestine Large	intestine

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