Variant report

Variant	rs10778323
Chromosome Location	chr12:104746075-104746076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104680804..104683254-chr12:104744568..104746415,2	K562	blood:
2	chr12:104733554..104735201-chr12:104744621..104746715,2	K562	blood:
3	chr12:104744585..104747269-chr12:104747658..104751523,4	K562	blood:
4	chr12:104744585..104746510-chr12:104748282..104749996,2	K562	blood:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10735392	0.81[CEU][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs10735393	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs10735394	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10745995	0.81[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs10745996	0.81[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs10745999	0.83[ASN][1000 genomes]
rs10778311	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs10778318	0.83[JPT][hapmap]
rs10861202	0.90[ASN][1000 genomes]
rs10861204	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11111955	0.80[CEU][hapmap]
rs11111960	0.83[JPT][hapmap]
rs11111963	0.91[JPT][hapmap]
rs17035372	0.94[YRI][hapmap]
rs34518697	0.96[AFR][1000 genomes]
rs34612644	0.92[AFR][1000 genomes]
rs35764486	0.96[AFR][1000 genomes]
rs4246269	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4246271	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4406890	0.82[CEU][hapmap]
rs4477504	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964288	0.81[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[ASN][1000 genomes]
rs4964728	0.82[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs4964735	0.83[JPT][hapmap]
rs4964752	0.81[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs4964761	0.81[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs4964779	0.81[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4964781	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539136	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6539138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7138035	0.84[CEU][hapmap]
rs7138523	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs7301631	0.92[JPT][hapmap]
rs7303284	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7309973	0.82[YRI][hapmap];0.94[AFR][1000 genomes]
rs7316394	0.81[ASN][1000 genomes]
rs7342395	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs7958103	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7962423	0.81[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap]
rs7975161	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs9739833	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10778323	NR1H4	cis	cerebellum	SCAN

Chromatin state (count:120 , 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	chr12:104702400-104746600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:104702400-104747400	Strong transcription	Dnd41	blood
4	chr12:104703000-104749200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:104703400-104747800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:104704800-104747200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:104709800-104749200	Strong transcription	HUVEC	blood vessel
8	chr12:104717600-104746200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:104717800-104746400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:104717800-104747600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr12:104717800-104748000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:104718400-104746200	Strong transcription	Hela-S3	cervix
13	chr12:104721800-104760000	Weak transcription	Stomach Mucosa	stomach
14	chr12:104725000-104749400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:104726800-104747200	Strong transcription	HepG2	liver
16	chr12:104727200-104746200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:104727200-104747200	Strong transcription	Fetal Thymus	thymus
18	chr12:104727200-104747400	Strong transcription	Liver	Liver
19	chr12:104727200-104748600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:104727400-104747200	Strong transcription	Placenta	Placenta
21	chr12:104727400-104747600	Strong transcription	NHEK	skin
22	chr12:104727400-104748600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:104727400-104749000	Strong transcription	HMEC	breast
24	chr12:104728800-104755000	Weak transcription	Fetal Heart	heart
25	chr12:104730400-104747800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:104732200-104746400	Strong transcription	Primary hematopoietic stem cells	blood
27	chr12:104732800-104747000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr12:104732800-104748200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:104734000-104750400	Weak transcription	Fetal Brain Male	brain
30	chr12:104734600-104747200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:104735200-104749000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:104736800-104747400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:104738600-104746200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:104738800-104746800	Genic enhancers	A549	lung
35	chr12:104738800-104748600	Strong transcription	NH-A	brain
36	chr12:104739000-104746200	Strong transcription	Fetal Intestine Small	intestine
37	chr12:104739000-104746200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:104739200-104746200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr12:104739200-104746400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:104739400-104749600	Strong transcription	HSMM	muscle
41	chr12:104739600-104749000	Strong transcription	Thymus	Thymus
42	chr12:104739800-104746200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:104740200-104749000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:104740200-104749200	Strong transcription	HSMMtube	muscle
45	chr12:104741000-104746200	Strong transcription	Colon Smooth Muscle	Colon
46	chr12:104741000-104746600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:104741000-104746600	Strong transcription	K562	blood
48	chr12:104741000-104747800	Strong transcription	Primary B cells from cord blood	blood
49	chr12:104741000-104749200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:104741000-104749200	Strong transcription	NHLF	lung

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