Variant report

Variant	rs347904
Chromosome Location	chr1:120177620-120177621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120177493..120182288-chr1:120186633..120192324,9	MCF-7	breast:
2	chr1:120169996..120174289-chr1:120174706..120179786,6	MCF-7	breast:
3	chr1:120174871..120178397-chr1:120178450..120180303,3	K562	blood:
4	chr1:120177198..120184772-chr1:120188907..120196947,14	MCF-7	breast:
5	chr1:120176290..120178351-chr1:120198069..120200672,2	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	0.89[JPT][hapmap]
rs10754417	0.89[JPT][hapmap]
rs347909	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs347911	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs376910	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs377033	0.89[JPT][hapmap]
rs431441	0.84[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs454510	0.89[JPT][hapmap]
rs496886	0.89[JPT][hapmap]
rs7531516	0.84[ASN][1000 genomes]
rs838986	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]
rs838987	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs838989	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs838990	0.89[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:82 , 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	chr1:120169000-120178400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:120169400-120178400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:120169400-120184400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:120174800-120182000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr1:120174800-120186000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:120175000-120178600	Weak transcription	Esophagus	oesophagus
10	chr1:120175000-120178600	Weak transcription	Small Intestine	intestine
11	chr1:120175000-120181800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:120175000-120182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:120175000-120182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:120175000-120183000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:120175200-120178400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:120175200-120178400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:120175200-120178600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:120175200-120179200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:120175200-120180200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:120175200-120180200	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:120175200-120183000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:120175200-120188200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:120175400-120178400	Weak transcription	NHEK	skin
24	chr1:120175400-120178600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:120175400-120178600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:120175400-120178800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:120175400-120178800	Weak transcription	Gastric	stomach
28	chr1:120175400-120179400	Weak transcription	Fetal Intestine Large	intestine
29	chr1:120175400-120179400	Weak transcription	Pancreas	Pancrea
30	chr1:120175400-120180200	Weak transcription	Fetal Brain Female	brain
31	chr1:120175400-120182000	Weak transcription	Placenta	Placenta
32	chr1:120175400-120186000	Weak transcription	Aorta	Aorta
33	chr1:120175400-120188000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:120175400-120188200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:120175400-120189200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:120175600-120178600	Weak transcription	NH-A	brain
37	chr1:120175600-120181800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:120175600-120182800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:120175600-120187800	Weak transcription	HMEC	breast
40	chr1:120175600-120188200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:120175800-120178400	Enhancers	HUVEC	blood vessel
42	chr1:120175800-120178600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:120175800-120178600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:120175800-120179200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:120175800-120181000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:120175800-120188000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:120176000-120188400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:120176200-120178200	Enhancers	Fetal Heart	heart
49	chr1:120176200-120178600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:120176200-120178600	Weak transcription	Fetal Brain Male	brain

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