Variant report

Variant	rs10861404
Chromosome Location	chr12:105746128-105746129
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	TCF12	chr12:105745817-105746231	GM12878	blood:	n/a	n/a
2	BATF	chr12:105745917-105746230	GM12878	blood:	n/a	n/a
3	SPI1	chr12:105745855-105746210	GM12878	blood:	n/a	n/a
4	EP300	chr12:105745796-105746258	GM12878	blood:	n/a	chr12:105745972-105745986 chr12:105746068-105746082 chr12:105745995-105746002
5	IRF4	chr12:105745766-105746212	GM12878	blood:	n/a	n/a
6	YY1	chr12:105745761-105746190	GM12892	blood:	n/a	n/a
7	BCL11A	chr12:105745760-105746255	GM12878	blood:	n/a	n/a
8	ATF2	chr12:105745785-105746226	GM12878	blood:	n/a	n/a
9	WRNIP1	chr12:105745928-105746171	GM12878	blood:	n/a	n/a
10	EBF1	chr12:105745777-105746206	GM12878	blood:	n/a	chr12:105746018-105746029 chr12:105746019-105746029
11	ELF1	chr12:105745820-105746158	GM12878	blood:	n/a	n/a
12	YY1	chr12:105745592-105746196	GM12878	blood:	n/a	n/a
13	FOXM1	chr12:105745660-105746382	GM12878	blood:	n/a	n/a
14	FOXM1	chr12:105745723-105746334	GM12878	blood:	n/a	n/a
15	NFIC	chr12:105745757-105746568	GM12878	blood:	n/a	n/a
16	ZNF143	chr12:105745834-105746169	GM12878	blood:	n/a	chr12:105746017-105746035
17	PML	chr12:105745481-105746285	GM12878	blood:	n/a	n/a
18	MTA3	chr12:105745715-105746340	GM12878	blood:	n/a	n/a
19	PAX5	chr12:105745884-105746158	GM12878	blood:	n/a	n/a
20	SPI1	chr12:105745813-105746202	GM12891	blood:	n/a	n/a
21	RELA	chr12:105745647-105746619	GM19099	blood:	n/a	n/a
22	EP300	chr12:105745794-105746227	GM12878	blood:	n/a	chr12:105745972-105745986 chr12:105746068-105746082 chr12:105745995-105746002
23	ATF2	chr12:105745773-105746233	GM12878	blood:	n/a	n/a
24	RUNX3	chr12:105745614-105746312	GM12878	blood:	n/a	n/a
25	IKZF1	chr12:105745520-105746312	GM12878	blood:	n/a	n/a
26	SPI1	chr12:105745974-105746138	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:105746064-105746142	ProgFib	skin:	n/a	n/a
28	EBF1	chr12:105745844-105746207	GM12878	blood:	n/a	chr12:105746018-105746029 chr12:105746019-105746029
29	TCF12	chr12:105745872-105746214	GM12878	blood:	n/a	n/a
30	MTA3	chr12:105745715-105746182	GM12878	blood:	n/a	n/a
31	YY1	chr12:105745768-105746192	GM12878	blood:	n/a	n/a
32	PAX5	chr12:105745853-105746155	GM12878	blood:	n/a	n/a
33	NFIC	chr12:105745705-105746375	GM12878	blood:	n/a	n/a
34	BATF	chr12:105745789-105746206	GM12878	blood:	n/a	n/a
35	EBF1	chr12:105745405-105746245	GM12878	blood:	n/a	chr12:105746018-105746029 chr12:105746019-105746029
36	YY1	chr12:105745808-105746171	GM12892	blood:	n/a	n/a
37	EP300	chr12:105745837-105746283	GM12878	blood:	n/a	chr12:105745972-105745986 chr12:105746068-105746082 chr12:105745995-105746002
38	PAX5	chr12:105745752-105746186	GM12878	blood:	n/a	n/a
39	TCF3	chr12:105745849-105746241	GM12878	blood:	n/a	n/a
40	TCF3	chr12:105745873-105746201	GM12878	blood:	n/a	n/a
41	BCL11A	chr12:105745868-105746174	GM12878	blood:	n/a	n/a
42	YY1	chr12:105745827-105746185	GM12891	blood:	n/a	n/a
43	SPI1	chr12:105745779-105746163	GM12891	blood:	n/a	n/a
44	IRF4	chr12:105745706-105746207	GM12878	blood:	n/a	n/a
45	SP1	chr12:105745801-105746227	GM12878	blood:	n/a	n/a
46	RUNX3	chr12:105745344-105746331	GM12878	blood:	n/a	n/a
47	BCLAF1	chr12:105745775-105746292	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
C12orf75	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12312486	0.94[ASN][1000 genomes]
rs1344778	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.95[ASN][1000 genomes]
rs17188203	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4246251	0.96[ASN][1000 genomes]
rs4964360	0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4964363	0.82[ASN][1000 genomes]
rs61939073	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs715167	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7295277	0.95[ASN][1000 genomes]
rs73401756	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899500	chr12:105742674-105803028	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active 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	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10861404	KIAA1033	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105725600-105747200	Weak transcription	Gastric	stomach
2	chr12:105729800-105749400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:105730600-105755400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:105734800-105750200	Weak transcription	Primary T cells from cord blood	blood
5	chr12:105734800-105750800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:105734800-105776600	Weak transcription	Esophagus	oesophagus
7	chr12:105735000-105776600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:105735200-105750800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:105735400-105756800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:105735600-105746200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:105735600-105749200	Weak transcription	HMEC	breast
12	chr12:105735600-105750600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:105735600-105753800	Weak transcription	Fetal Stomach	stomach
14	chr12:105735600-105766800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:105735600-105776600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:105736200-105749200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:105738000-105752000	Weak transcription	Spleen	Spleen
18	chr12:105738200-105746400	Weak transcription	NH-A	brain
19	chr12:105738200-105750600	Weak transcription	Primary B cells from cord blood	blood
20	chr12:105741800-105750800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:105743200-105746400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:105743400-105746200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:105743400-105746400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:105743800-105747200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:105744000-105746400	Strong transcription	HSMM	muscle
26	chr12:105744400-105746800	Weak transcription	HSMMtube	muscle
27	chr12:105744400-105749000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:105744400-105749000	Genic enhancers	NHDF-Ad	bronchial
29	chr12:105744400-105750800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:105744600-105746400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:105744600-105749200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:105744800-105746600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:105745200-105746400	Flanking Active TSS	GM12878-XiMat	blood
34	chr12:105745200-105746600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:105745200-105747400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:105745200-105747400	Enhancers	Aorta	Aorta
37	chr12:105745400-105746200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:105745400-105746200	Enhancers	Primary T cells fromperipheralblood	blood
39	chr12:105745400-105746200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:105745400-105746600	Flanking Active TSS	Dnd41	blood
41	chr12:105745400-105746800	Enhancers	Psoas Muscle	Psoas
42	chr12:105745400-105747200	Enhancers	Primary B cells from peripheral blood	blood
43	chr12:105745400-105747200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:105745400-105747200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:105745400-105747400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:105745400-105747400	Enhancers	Thymus	Thymus
47	chr12:105745600-105746800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:105745600-105746800	Weak transcription	Pancreas	Pancrea
49	chr12:105745600-105747000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:105745600-105747400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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