Variant report

Variant	rs9863738
Chromosome Location	chr3:99982607-99982608
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	IRF1	chr3:99982580-99982850	K562	blood:	n/a	chr3:99982790-99982803 chr3:99982785-99982802 chr3:99982790-99982803 chr3:99982791-99982801 chr3:99982789-99982803 chr3:99982789-99982800 chr3:99982790-99982803 chr3:99982787-99982801 chr3:99982791-99982805 chr3:99982790-99982804 chr3:99982790-99982801
2	IRF1	chr3:99982535-99982967	K562	blood:	n/a	chr3:99982790-99982803 chr3:99982785-99982802 chr3:99982790-99982803 chr3:99982791-99982801 chr3:99982789-99982803 chr3:99982789-99982800 chr3:99982790-99982803 chr3:99982787-99982801 chr3:99982791-99982805 chr3:99982790-99982804 chr3:99982790-99982801
3	EBF1	chr3:99982450-99982871	GM12878	blood:	n/a	chr3:99982647-99982658
4	GATA1	chr3:99981537-99983408	PBDE	blood:	n/a	chr3:99983275-99983284

No.	Distal block	Cell Line	Cell type
1	chr3:99979844..99981750-chr3:99981771..99983901,2	MCF-7	breast:
2	chr3:99981876..99985966-chr3:99986124..99992664,8	K562	blood:
3	chr3:99591850..99594536-chr3:99980465..99982700,2	K562	blood:
4	chr3:99571584..99573287-chr3:99980510..99983253,2	K562	blood:
5	chr3:99614799..99616981-chr3:99982145..99984761,2	K562	blood:
6	chr3:99982526..99986006-chr3:99993690..99996529,5	K562	blood:
7	chr3:99614799..99617137-chr3:99982145..99984761,3	K562	blood:
8	chr3:99981806..99984412-chr3:100006870..100008819,2	K562	blood:

Variant related genes	Relation type
TBC1D23	TF binding region
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1036770	0.83[EUR][1000 genomes]
rs10936157	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11915985	0.83[EUR][1000 genomes]
rs1214369	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214372	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214373	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12696064	1.00[ASN][1000 genomes]
rs12696084	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070392	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1609481	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2028494	0.89[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2029163	1.00[ASN][1000 genomes]
rs277636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277654	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35950794	1.00[ASN][1000 genomes]
rs3772698	0.88[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs4552390	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4928119	0.89[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4928169	0.89[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs62281675	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763594	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777265	0.95[ASN][1000 genomes]
rs6802765	0.86[EUR][1000 genomes]
rs6808175	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7427443	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618677	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630257	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637157	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638503	0.86[EUR][1000 genomes]
rs9289985	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs931332	0.85[EUR][1000 genomes]
rs967608	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs9854260	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs9860290	0.85[JPT][hapmap]
rs9875878	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs9880795	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882337	1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9863738	TBC1D23	cis	Muscle Skeletal	GTEx
rs9863738	ZPLD1	cis	parietal	SCAN
rs9863738	ZNF546	trans	parietal	SCAN
rs9863738	TBC1D23	cis	Heart Left Ventricle	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99979200-99982800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:99980600-99983200	Enhancers	Small Intestine	intestine
3	chr3:99980600-99983800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr3:99980600-99988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
6	chr3:99980600-100053200	Weak transcription	Gastric	stomach
7	chr3:99980800-99983000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:99980800-99983200	Enhancers	Brain Substantia Nigra	brain
9	chr3:99980800-99988800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:99981000-99983000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:99981000-99983400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr3:99981000-99983800	Weak transcription	Colonic Mucosa	Colon
13	chr3:99981000-99984400	Enhancers	Liver	Liver
14	chr3:99981000-99990400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:99981000-99996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:99981200-99982800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:99981200-99982800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:99981200-99982800	Enhancers	Fetal Intestine Large	intestine
19	chr3:99981200-99982800	Enhancers	Stomach Smooth Muscle	stomach
20	chr3:99981200-99983000	Enhancers	Fetal Intestine Small	intestine
21	chr3:99981200-99983200	Enhancers	Fetal Brain Male	brain
22	chr3:99981200-99983600	Weak transcription	Stomach Mucosa	stomach
23	chr3:99981200-99984000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:99981200-99984200	Enhancers	Adipose Nuclei	Adipose
25	chr3:99981200-99985200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:99981200-99985400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:99981200-99986000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:99981200-99987000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:99981200-99988600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:99981200-99988800	Weak transcription	Fetal Brain Female	brain
31	chr3:99981200-99993200	Weak transcription	Primary B cells from cord blood	blood
32	chr3:99981200-99995400	Weak transcription	Brain Angular Gyrus	brain
33	chr3:99981200-99997800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:99981200-99998400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:99981200-99998600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:99981200-99998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:99981200-100004800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
39	chr3:99981400-99986800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:99981400-99988600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:99981400-99998400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:99981400-100004400	Weak transcription	Lung	lung
43	chr3:99981600-99983000	Weak transcription	Left Ventricle	heart
44	chr3:99981800-99983800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:99982000-99982800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:99982000-99983000	Enhancers	Fetal Muscle Leg	muscle
47	chr3:99982000-99983200	Enhancers	Dnd41	blood
48	chr3:99982000-99984200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:99982000-99984200	Enhancers	Duodenum Mucosa	Duodenum
50	chr3:99982000-99986800	Weak transcription	Right Atrium	heart

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