Variant report

Variant	rs3748235
Chromosome Location	chr10:98379928-98379929
allele	A/G
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	chr10:98379785-98380078	GM12891	blood:	n/a	n/a
2	MAX	chr10:98379781-98380053	K562	blood:	n/a	n/a
3	POLR2A	chr10:98379904-98380950	GM12878	blood:	n/a	n/a
4	MYC	chr10:98379655-98379967	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA1	chr10:98378377-98380060	PBDE	blood:	n/a	n/a
6	NFIC	chr10:98379516-98379932	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr10:98378430-98380231	PBDE	blood:	n/a	n/a
8	POLR2A	chr10:98379744-98380474	GM12878	blood:	n/a	n/a
9	MYC	chr10:98379482-98379954	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98376679..98380080-chr10:98381155..98385346,4	MCF-7	breast:

Variant related genes	Relation type
PIK3AP1	TF binding region
ENSG00000227032	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1018604	0.92[JPT][hapmap]
rs1018605	0.96[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1051450	0.84[CHD][hapmap]
rs10736114	0.81[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882811	0.96[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs10882813	0.92[JPT][hapmap]
rs10882815	0.84[CHD][hapmap]
rs10882826	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10882827	0.84[ASN][1000 genomes]
rs10882828	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11188817	0.84[CHD][hapmap]
rs11188822	0.84[JPT][hapmap]
rs11188825	0.84[CHD][hapmap]
rs11188847	0.84[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188853	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11188854	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11188856	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188857	0.96[ASN][1000 genomes]
rs1132913	0.84[CHD][hapmap]
rs12219275	0.80[CHD][hapmap]
rs12416646	0.80[CHD][hapmap]
rs12779720	0.84[CHD][hapmap]
rs1324261	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1408367	0.84[CHD][hapmap]
rs1983831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33964467	0.84[CHD][hapmap]
rs35779764	0.84[CHD][hapmap]
rs3748234	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748236	0.80[ASN][1000 genomes]
rs3789957	0.92[JPT][hapmap]
rs3818389	0.92[JPT][hapmap]
rs4146727	0.84[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4485036	0.84[CHD][hapmap]
rs4534508	0.84[CHD][hapmap]
rs4917742	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919029	0.96[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs4919032	0.92[JPT][hapmap]
rs4919040	0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7069429	0.80[CHD][hapmap]
rs7071044	0.84[CHD][hapmap]
rs7074516	0.84[CHD][hapmap]
rs7091606	0.84[CHD][hapmap]
rs7101320	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs713251	0.84[CHD][hapmap]
rs727329	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7448	0.83[ASW][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs7478356	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7914154	0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7919739	0.92[JPT][hapmap]
rs8578	0.84[CHD][hapmap]
rs912480	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs927639	0.89[ASW][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9633703	0.96[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs9664749	0.84[CHD][hapmap]

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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv895909	chr10:98354924-98382165	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3748235	NPM1P26	cis	Stomach	GTEx
rs3748235	NPM1P26	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98350800-98395600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr10:98352400-98399400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr10:98352600-98403000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr10:98353000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:98353000-98403000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr10:98354600-98388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:98357800-98382000	Strong transcription	GM12878-XiMat	blood
8	chr10:98360400-98392800	Weak transcription	Thymus	Thymus
9	chr10:98362200-98389200	Strong transcription	Primary B cells from cord blood	blood
10	chr10:98363800-98392600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:98366000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:98366600-98392600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:98367400-98418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr10:98371000-98382600	Strong transcription	Spleen	Spleen
15	chr10:98371000-98388600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr10:98371000-98389000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:98372200-98388600	Strong transcription	Primary hematopoietic stem cells	blood
18	chr10:98374400-98390200	Weak transcription	Small Intestine	intestine
19	chr10:98375600-98380800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr10:98375800-98390200	Weak transcription	Adipose Nuclei	Adipose
21	chr10:98376400-98380400	Enhancers	Fetal Heart	heart
22	chr10:98376400-98381200	Enhancers	Ovary	ovary
23	chr10:98376600-98380400	Enhancers	Left Ventricle	heart
24	chr10:98376800-98381000	Enhancers	Right Atrium	heart
25	chr10:98377000-98380800	Enhancers	Fetal Lung	lung
26	chr10:98377200-98380000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr10:98377200-98380000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr10:98377200-98384400	Enhancers	Stomach Mucosa	stomach
29	chr10:98377400-98380000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr10:98377400-98392600	Weak transcription	Esophagus	oesophagus
31	chr10:98377600-98380400	Enhancers	Colon Smooth Muscle	Colon
32	chr10:98378000-98380000	Enhancers	Stomach Smooth Muscle	stomach
33	chr10:98378200-98392600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:98378400-98380000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr10:98378400-98380000	Enhancers	Fetal Brain Male	brain
36	chr10:98378400-98380000	Enhancers	Rectal Smooth Muscle	rectum
37	chr10:98378400-98380200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:98378400-98380200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr10:98378400-98380200	Enhancers	HSMM	muscle
40	chr10:98378400-98380400	Enhancers	Duodenum Mucosa	Duodenum
41	chr10:98378400-98381200	Enhancers	Right Ventricle	heart
42	chr10:98378600-98380000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr10:98378600-98380200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:98378600-98381000	Enhancers	Colonic Mucosa	Colon
45	chr10:98378600-98382000	Enhancers	Gastric	stomach
46	chr10:98378800-98381400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:98378800-98389400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:98378800-98392400	Weak transcription	Fetal Intestine Large	intestine
49	chr10:98378800-98392600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr10:98379000-98381800	Weak transcription	Brain Substantia Nigra	brain

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