Variant report

Variant	rs10936162
Chromosome Location	chr3:158536123-158536124
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	CEBPB	chr3:158536049-158536221	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
MFSD1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10513528	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs10936160	0.80[AFR][1000 genomes]
rs10936161	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12054172	0.83[JPT][hapmap]
rs12493280	0.86[LWK][hapmap];0.80[AFR][1000 genomes]
rs12497958	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28364680	0.99[ASN][1000 genomes]
rs41272621	1.00[ASN][1000 genomes]
rs41434057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55705231	0.89[EUR][1000 genomes]
rs56261306	0.87[EUR][1000 genomes]
rs56857471	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61796762	0.89[EUR][1000 genomes]
rs61796764	0.89[EUR][1000 genomes]
rs61796766	0.89[EUR][1000 genomes]
rs61796775	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61796802	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6441226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7429205	0.82[AFR][1000 genomes]
rs7624420	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs7624702	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10936162	LXN	cis	multi-tissue	Pritchard
rs10936162	LXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158520400-158552400	Weak transcription	Stomach Mucosa	stomach
2	chr3:158520600-158543400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:158520800-158545400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:158521000-158543200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:158521400-158544400	Weak transcription	HepG2	liver
6	chr3:158522400-158550000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:158523000-158544000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:158526600-158539800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:158527800-158543200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:158527800-158554000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:158528000-158541400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:158528000-158547000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:158528000-158549400	Weak transcription	Dnd41	blood
14	chr3:158528600-158549600	Weak transcription	Fetal Kidney	kidney
15	chr3:158528800-158541200	Weak transcription	K562	blood
16	chr3:158528800-158547200	Weak transcription	Psoas Muscle	Psoas
17	chr3:158529000-158539400	Weak transcription	Fetal Brain Female	brain
18	chr3:158529400-158544800	Weak transcription	Hela-S3	cervix
19	chr3:158529600-158538800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:158529600-158544200	Weak transcription	Fetal Heart	heart
21	chr3:158530400-158538200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:158530400-158543800	Weak transcription	Fetal Brain Male	brain
23	chr3:158530600-158541600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:158530800-158538400	Weak transcription	Aorta	Aorta
25	chr3:158530800-158539400	Weak transcription	HSMMtube	muscle
26	chr3:158530800-158541200	Weak transcription	Brain Germinal Matrix	brain
27	chr3:158531400-158538400	Weak transcription	Small Intestine	intestine
28	chr3:158531800-158537000	Weak transcription	Brain Substantia Nigra	brain
29	chr3:158532000-158536600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:158532000-158536800	Weak transcription	NH-A	brain
31	chr3:158532000-158538400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:158532000-158538600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:158532000-158539600	Weak transcription	Fetal Lung	lung
34	chr3:158532000-158541200	Weak transcription	Colonic Mucosa	Colon
35	chr3:158532000-158541400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:158532200-158536800	Weak transcription	NHDF-Ad	bronchial
37	chr3:158532200-158551800	Weak transcription	NHEK	skin
38	chr3:158532400-158557800	Weak transcription	Gastric	stomach
39	chr3:158532800-158538400	Weak transcription	Ovary	ovary
40	chr3:158532800-158539600	Weak transcription	Spleen	Spleen
41	chr3:158533000-158536400	Weak transcription	Left Ventricle	heart
42	chr3:158533000-158538000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:158533000-158541200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:158533000-158541200	Weak transcription	Esophagus	oesophagus
45	chr3:158533000-158543000	Weak transcription	Fetal Intestine Small	intestine
46	chr3:158533000-158543000	Weak transcription	Fetal Stomach	stomach
47	chr3:158533000-158548000	Weak transcription	Pancreas	Pancrea
48	chr3:158533000-158551000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:158533000-158556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:158533000-158559600	Weak transcription	Right Ventricle	heart

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