Variant report

Variant	rs12140423
Chromosome Location	chr1:224562931-224562932
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224562792..224564765-chr1:224585546..224588270,2	K562	blood:
2	chr1:224561356..224563352-chr1:224578652..224580931,2	K562	blood:
3	chr1:224543721..224546086-chr1:224562908..224565121,2	MCF-7	breast:
4	chr1:224559204..224561401-chr1:224561938..224564303,3	MCF-7	breast:
5	chr1:224544599..224546444-chr1:224561774..224564009,2	K562	blood:
6	chr1:224544372..224546444-chr1:224561332..224563274,2	K562	blood:

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction
ENSG00000266618	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10495220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10799574	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12075578	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120702	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121977	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12124686	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12128292	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684878	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72758316	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
2	chr1:224546000-224563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
5	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:224547800-224568600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
8	chr1:224550400-224568000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:224550800-224564200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:224550800-224565000	Strong transcription	HUVEC	blood vessel
11	chr1:224551000-224568000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:224551200-224563600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:224551200-224565800	Strong transcription	Primary B cells from cord blood	blood
14	chr1:224551400-224568600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:224551600-224566600	Strong transcription	Dnd41	blood
16	chr1:224551600-224568000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:224551600-224568400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:224552000-224564800	Weak transcription	Psoas Muscle	Psoas
19	chr1:224552600-224563800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:224552800-224564200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:224552800-224565800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:224553000-224564200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:224553000-224565000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:224553000-224565200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:224553200-224564400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:224553200-224567400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:224553400-224565000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:224553400-224567000	Strong transcription	Adipose Nuclei	Adipose
29	chr1:224553400-224567400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:224553600-224564400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:224553600-224566000	Strong transcription	Fetal Intestine Large	intestine
32	chr1:224553600-224566400	Strong transcription	Fetal Intestine Small	intestine
33	chr1:224553800-224564200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:224553800-224568800	Strong transcription	Fetal Stomach	stomach
35	chr1:224554200-224565600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr1:224554400-224563600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:224554400-224568200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr1:224554600-224564200	Strong transcription	NHDF-Ad	bronchial
39	chr1:224554600-224567200	Strong transcription	Liver	Liver
40	chr1:224554600-224567400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:224554800-224563800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:224554800-224568600	Strong transcription	Fetal Brain Female	brain
43	chr1:224555000-224564400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:224555000-224568000	Strong transcription	Brain Anterior Caudate	brain
45	chr1:224555000-224568200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:224555200-224564200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:224555200-224564400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr1:224555200-224566000	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr1:224555200-224568000	Strong transcription	Brain Germinal Matrix	brain
50	chr1:224555400-224565400	Strong transcription	HepG2	liver

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