Variant report

Variant	rs10778322
Chromosome Location	chr12:104725577-104725578
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	chr12:104722655-104726434	A549	lung:	n/a	n/a
2	POLR2A	chr12:104725563-104725804	HCT-116	colon:	n/a	n/a
3	POLR2A	chr12:104724656-104726045	K562	blood:	n/a	n/a
4	POLR2A	chr12:104725542-104725725	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:104722565-104726342	HepG2	liver:	n/a	n/a
6	BCL3	chr12:104724952-104726093	A549	lung:	n/a	chr12:104725860-104725869

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104714658..104717606-chr12:104724030..104726701,2	K562	blood:

Variant related genes	Relation type
TXNRD1	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10047589	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861186	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861200	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10861201	0.87[GIH][hapmap]
rs11111993	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610799	0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11610993	0.82[JPT][hapmap]
rs11611385	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12305190	0.82[JPT][hapmap]
rs34015677	0.92[ASN][1000 genomes]
rs34615738	0.92[ASN][1000 genomes]
rs34621285	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35359688	0.90[ASN][1000 genomes]
rs4411337	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4523760	0.84[GIH][hapmap]
rs4564401	0.86[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4964287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7138318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294412	0.92[ASN][1000 genomes]
rs7300638	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73180130	0.90[ASN][1000 genomes]
rs73181910	0.86[ASN][1000 genomes]
rs73181913	0.87[ASN][1000 genomes]
rs7962942	0.84[GIH][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	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10778322	TDG	cis	parietal	SCAN
rs10778322	TCP11L2	cis	cerebellum	SCAN
rs10778322	PMCH	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104698400-104747600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:104699400-104728400	Weak transcription	Fetal Heart	heart
3	chr12:104701600-104733600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:104702000-104733600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:104702400-104746600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:104702400-104747400	Strong transcription	Dnd41	blood
7	chr12:104703000-104749200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:104703400-104738400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:104703400-104747800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:104703600-104744000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:104703800-104733000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:104704400-104743600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:104704800-104726400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:104704800-104747200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:104705000-104726000	Strong transcription	Placenta	Placenta
16	chr12:104705000-104726400	Strong transcription	Liver	Liver
17	chr12:104708400-104728400	Strong transcription	Osteobl	bone
18	chr12:104709800-104732800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:104709800-104749200	Strong transcription	HUVEC	blood vessel
20	chr12:104714200-104728200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:104715400-104726200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:104715600-104734800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:104716200-104727400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr12:104716400-104736600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:104717400-104726000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:104717400-104726000	Strong transcription	NHLF	lung
27	chr12:104717600-104744600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:104717600-104746200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:104717800-104726000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:104717800-104726000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr12:104717800-104726000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr12:104717800-104726000	Strong transcription	NHEK	skin
33	chr12:104717800-104727600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr12:104717800-104733400	Strong transcription	HSMM	muscle
35	chr12:104717800-104744000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:104717800-104746400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:104717800-104747600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:104717800-104748000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:104718400-104746200	Strong transcription	Hela-S3	cervix
40	chr12:104718600-104737200	Strong transcription	NHDF-Ad	bronchial
41	chr12:104718800-104726200	Genic enhancers	A549	lung
42	chr12:104719400-104727400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:104720600-104739000	Strong transcription	GM12878-XiMat	blood
44	chr12:104721000-104728200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:104721400-104728400	Weak transcription	Right Ventricle	heart
46	chr12:104721600-104727400	Weak transcription	Primary B cells from cord blood	blood
47	chr12:104721600-104728000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:104721600-104728000	Weak transcription	Brain Angular Gyrus	brain
49	chr12:104721600-104728200	Weak transcription	Colonic Mucosa	Colon
50	chr12:104721600-104729800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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