Variant report

Variant	rs2074534
Chromosome Location	chr12:48133563-48133564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr12:48133414-48134775	GM12878	blood:	n/a	n/a
2	MTA3	chr12:48133560-48134651	GM12878	blood:	n/a	n/a
3	ZNF263	chr12:48133547-48134655	K562	blood:	n/a	n/a
4	POLR2A	chr12:48133458-48135692	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48133250..48135553-chr12:48296742..48299315,2	K562	blood:
2	chr12:48128880..48137705-chr12:48169546..48175532,12	K562	blood:
3	chr12:48133209..48136160-chr12:48165338..48168109,2	K562	blood:
4	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:

No data

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000111424	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11168220	0.84[AFR][1000 genomes]
rs2074533	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285830	0.81[LWK][hapmap]
rs7306680	0.87[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2074534	ARID2	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48114000-48134400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:48115600-48133600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:48115600-48134200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:48115600-48135000	Weak transcription	Primary T cells from cord blood	blood
5	chr12:48116200-48134000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:48127000-48134000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:48127600-48135800	Enhancers	Fetal Muscle Trunk	muscle
8	chr12:48128200-48135600	Enhancers	Right Atrium	heart
9	chr12:48128400-48135000	Weak transcription	NHEK	skin
10	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:48129200-48134000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:48129200-48134600	Weak transcription	Fetal Brain Female	brain
13	chr12:48129200-48137600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:48129400-48134000	Weak transcription	Fetal Brain Male	brain
15	chr12:48129400-48134200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:48129400-48138600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:48129800-48137600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
20	chr12:48130200-48134800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:48130400-48134600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:48130400-48137600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:48130600-48133600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:48130600-48138800	Weak transcription	Fetal Intestine Large	intestine
25	chr12:48130800-48133600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:48130800-48134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:48131000-48133600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:48131000-48134600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
30	chr12:48131200-48133800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:48131200-48141600	Weak transcription	Fetal Kidney	kidney
32	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:48131400-48133600	Enhancers	Brain Germinal Matrix	brain
34	chr12:48131400-48133600	Weak transcription	Esophagus	oesophagus
35	chr12:48131400-48133600	Weak transcription	Psoas Muscle	Psoas
36	chr12:48131400-48133600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr12:48131400-48134400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:48131400-48134800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:48131600-48133600	Weak transcription	Colonic Mucosa	Colon
40	chr12:48131600-48134000	Weak transcription	Fetal Lung	lung
41	chr12:48131600-48134000	Weak transcription	HUVEC	blood vessel
42	chr12:48131600-48134200	Weak transcription	Fetal Intestine Small	intestine
43	chr12:48131600-48134400	Weak transcription	HSMMtube	muscle
44	chr12:48131600-48134800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr12:48131600-48134800	Weak transcription	Stomach Mucosa	stomach
46	chr12:48131600-48134800	Weak transcription	HSMM	muscle
47	chr12:48131600-48135000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:48131600-48135000	Weak transcription	Osteobl	bone
49	chr12:48131600-48135200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:48131600-48136400	Enhancers	Skeletal Muscle Male	skeletal muscle

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