Variant report

Variant	rs12070041
Chromosome Location	chr1:120280554-120280555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:120278647-120280610	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:120277856-120280604	K562	blood:	n/a	n/a
3	POLR2A	chr1:120278723-120281203	HepG2	liver:	n/a	n/a
4	GATA1	chr1:120279077-120280684	K562	blood:	n/a	chr1:120279992-120280009 chr1:120280003-120280010 chr1:120279999-120280012
5	USF2	chr1:120280264-120280670	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:120280500-120280564	K562	blood:	n/a	n/a
7	POLR2A	chr1:120272990-120290073	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:120272269-120288857	K562	blood:	n/a	n/a
9	POLR2A	chr1:120280010-120280851	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:120278363..120280873-chr1:120284153..120287954,3	K562	blood:
2	chr1:120274619..120277352-chr1:120278861..120281353,2	K562	blood:
3	chr1:120279084..120281873-chr1:120323241..120326193,2	MCF-7	breast:
4	chr1:120278740..120281495-chr1:120284812..120287109,2	MCF-7	breast:
5	chr1:120280233..120281890-chr1:120349060..120351958,2	K562	blood:
6	chr1:120253275..120257099-chr1:120276679..120281090,4	K562	blood:

Variant related genes	Relation type
PHGDH	TF binding region
ENSG00000092621	Chromatin interaction
ENSG00000134193	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10923897	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11487674	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12079115	1.00[CEU][hapmap]
rs12406668	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2236399	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2236400	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2241868	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9943291	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
2	chr1:120257000-120282400	Weak transcription	A549	lung
3	chr1:120257200-120287000	Weak transcription	NH-A	brain
4	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:120260400-120287600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:120261000-120287200	Strong transcription	Hela-S3	cervix
7	chr1:120261600-120288200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:120261800-120281600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:120261800-120287000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:120261800-120287600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:120262000-120284600	Strong transcription	Fetal Stomach	stomach
12	chr1:120262000-120287200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:120262000-120287400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:120262000-120287400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:120262000-120287800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:120262000-120288200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:120262200-120284400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:120262400-120283600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:120262400-120285000	Strong transcription	NHEK	skin
20	chr1:120262400-120287400	Strong transcription	Dnd41	blood
21	chr1:120262400-120288200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:120262600-120282800	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr1:120262600-120283800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:120262800-120281200	Strong transcription	Fetal Lung	lung
25	chr1:120263200-120286400	Strong transcription	Thymus	Thymus
26	chr1:120263400-120286800	Strong transcription	Primary T cells from cord blood	blood
27	chr1:120263400-120287400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:120263400-120291400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:120264000-120283800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:120266200-120282600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:120267200-120286800	Weak transcription	Primary B cells from cord blood	blood
32	chr1:120269800-120286800	Weak transcription	Small Intestine	intestine
33	chr1:120271000-120286600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:120271200-120286200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:120272800-120281400	Weak transcription	HUVEC	blood vessel
36	chr1:120272800-120285200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:120274000-120286400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:120274600-120282200	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr1:120275200-120284800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:120275200-120286800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:120275400-120280600	Enhancers	Brain Angular Gyrus	brain
42	chr1:120275400-120284400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:120275600-120281000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:120275600-120285000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:120275800-120286200	Strong transcription	HepG2	liver
46	chr1:120276400-120282000	Strong transcription	Aorta	Aorta
47	chr1:120276400-120285200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:120276400-120285800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:120276600-120281200	Genic enhancers	Pancreas	Pancrea
50	chr1:120276600-120282000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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