Variant report

Variant	rs1873914
Chromosome Location	chr12:56379427-56379428
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56379207-56379586	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56373854..56376498-chr12:56378002..56380904,2	K562	blood:
2	chr12:56366797..56368622-chr12:56378270..56380653,2	MCF-7	breast:
3	chr12:56378791..56380809-chr12:56434636..56437217,3	MCF-7	breast:
4	chr12:56314656..56316887-chr12:56377244..56380237,2	MCF-7	breast:
5	chr12:56137294..56139429-chr12:56377696..56379845,2	K562	blood:
6	chr12:56375142..56377081-chr12:56377358..56380445,4	MCF-7	breast:
7	chr12:56374509..56377876-chr12:56378080..56382114,4	MCF-7	breast:

No data

Variant related genes	Relation type
RAB5B	TF binding region
ENSG00000237493	TF binding region
ENSG00000197728	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000257449	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1081975	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876864	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1131017	0.87[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1701704	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2048036	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2069408	0.95[CHB][hapmap]
rs2456973	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs61937247	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61937248	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61937249	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs705698	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[ASN][1000 genomes]
rs705699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705700	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705702	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs705704	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs772920	0.93[ASN][1000 genomes]
rs772921	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs773107	0.88[MEX][hapmap];0.80[AMR][1000 genomes]
rs773108	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs773109	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs773110	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs773111	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs773112	0.97[ASN][1000 genomes]
rs773114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs773125	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 target site	189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs1873914	FLJ20280	trans	multi-tissue	Pritchard
rs1873914	RPS26	cis	lymphoblastoid	seeQTL
rs1873914	ERBB3	cis	parietal	SCAN
rs1873914	SUOX	cis	lung	GTEx
rs1873914	LOC644934	trans	multi-tissue	Pritchard
rs1873914	CSRNP2	cis	parietal	SCAN
rs1873914	SUOX	cis	Esophagus Muscularis	GTEx
rs1873914	INHBC	cis	cerebellum	SCAN
rs1873914	SUOX	cis	Nerve Tibial	GTEx
rs1873914	MADCAM1	trans	multi-tissue	Pritchard
rs1873914	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs1873914	RPS26///RPS26L///LOC644166///LOC644191	cis	normal skin	skin_eQTL
rs1873914	SUOX	cis	multi-tissue	Pritchard
rs1873914	MAGEC1	trans	multi-tissue	Pritchard
rs1873914	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs1873914	AC034102.1	cis	Muscle Skeletal	GTEx
rs1873914	SUOX	cis	Artery Tibial	GTEx
rs1873914	RAB5B	cis	Muscle Skeletal	GTEx
rs1873914	SUOX	cis	cerebellum	SCAN
rs1873914	RPS26P10	trans	multi-tissue	Pritchard
rs1873914	SUOX	cis	Skin Sun Exposed Lower leg	GTEx
rs1873914	DNAJC14	cis	parietal	SCAN
rs1873914	HOXC8	cis	cerebellum	SCAN
rs1873914	LOC441377	trans	multi-tissue	Pritchard
rs1873914	RPS26	cis	multi-tissue	Pritchard
rs1873914	LOC441502	trans	multi-tissue	Pritchard
rs1873914	CCDC4	trans	multi-tissue	Pritchard
rs1873914	SUOX	cis	parietal	SCAN
rs1873914	ACVR1B	cis	parietal	SCAN
rs1873914	SUOX	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56368600-56383200	Weak transcription	Gastric	stomach
2	chr12:56369000-56383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:56369200-56380000	Weak transcription	Right Ventricle	heart
4	chr12:56369200-56380400	Weak transcription	Aorta	Aorta
5	chr12:56369200-56383600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:56369200-56384600	Weak transcription	Psoas Muscle	Psoas
7	chr12:56369400-56381000	Weak transcription	Small Intestine	intestine
8	chr12:56369400-56383400	Weak transcription	Pancreas	Pancrea
9	chr12:56369400-56384200	Weak transcription	Fetal Brain Male	brain
10	chr12:56369400-56389400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56369800-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:56370000-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:56370000-56389600	Strong transcription	Fetal Thymus	thymus
14	chr12:56370200-56389600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:56370400-56385000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:56370400-56388400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:56370600-56383200	Weak transcription	HepG2	liver
18	chr12:56370600-56383400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:56370600-56388200	Strong transcription	Dnd41	blood
20	chr12:56370600-56389600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:56370800-56383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:56371000-56379600	Weak transcription	Right Atrium	heart
23	chr12:56371400-56381800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:56371400-56389600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:56371600-56383400	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:56371600-56388800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:56371800-56383400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:56372000-56380800	Weak transcription	Ovary	ovary
29	chr12:56372400-56379600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:56372400-56390000	Strong transcription	Placenta	Placenta
31	chr12:56372800-56386200	Strong transcription	Fetal Intestine Large	intestine
32	chr12:56372800-56389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:56372800-56389600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:56372800-56389600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:56373200-56386600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr12:56373400-56389400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:56373400-56389600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:56373600-56383400	Weak transcription	Stomach Mucosa	stomach
39	chr12:56373600-56388600	Strong transcription	Liver	Liver
40	chr12:56373800-56386000	Strong transcription	Fetal Intestine Small	intestine
41	chr12:56374000-56388600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:56374000-56389600	Strong transcription	Fetal Stomach	stomach
43	chr12:56374200-56388800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:56375200-56381000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:56375400-56381600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:56375600-56380000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:56375600-56380200	Weak transcription	Spleen	Spleen
48	chr12:56375600-56380800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:56375600-56381200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:56375600-56381800	Weak transcription	Brain Angular Gyrus	brain

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