Variant report

Variant	rs775310
Chromosome Location	chr12:67684163-67684164
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	MAFF	chr12:67684145-67684567	HepG2	liver:	n/a	chr12:67684345-67684363
2	MAFK	chr12:67684061-67684692	GM12878	blood:	n/a	chr12:67684350-67684366 chr12:67684347-67684358 chr12:67684347-67684358 chr12:67684348-67684359 chr12:67684348-67684359 chr12:67684348-67684368 chr12:67684346-67684360 chr12:67684347-67684362 chr12:67684347-67684363

No.	Distal block	Cell Line	Cell type
1	chr12:67681823..67684693-chr12:67719727..67722113,2	K562	blood:
2	chr12:67678774..67680822-chr12:67683989..67686617,2	MCF-7	breast:
3	chr12:67682602..67685085-chr12:67687619..67689287,2	K562	blood:
4	chr12:67662696..67664703-chr12:67682661..67684692,2	MCF-7	breast:

Variant related genes	Relation type
CAND1	TF binding region
ENSG00000111530	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10506545	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1060350	0.89[GIH][hapmap]
rs1066387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066388	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066394	0.94[AFR][1000 genomes]
rs1066395	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1066404	0.93[GIH][hapmap]
rs10784625	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1082701	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1082702	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1082708	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1082709	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1082711	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1092475	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11176678	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176683	0.89[GIH][hapmap]
rs1143758	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1143947	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1143948	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1152877	0.89[GIH][hapmap]
rs1152896	0.93[GIH][hapmap]
rs1152900	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1152902	0.89[GIH][hapmap]
rs1161088	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1161092	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1177317	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252402	0.93[GIH][hapmap]
rs1252404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252405	0.89[GIH][hapmap]
rs1252406	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252414	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252418	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1252423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12580790	0.89[GIH][hapmap]
rs1272090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1392587	0.89[GIH][hapmap]
rs1500433	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1561334	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1621634	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1658780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985475	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2438108	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4913538	0.89[GIH][hapmap]
rs698123	0.93[GIH][hapmap]
rs710622	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710623	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs710797	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs710798	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs710801	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775307	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs775308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs775628	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775634	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs775635	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs775645	0.93[GIH][hapmap]
rs775646	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775647	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775648	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs775650	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775653	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775654	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775656	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775657	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775658	0.97[ASN][1000 genomes]
rs775659	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957112	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7962358	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7962587	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs796508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs796521	0.82[YRI][hapmap]
rs7973565	0.89[GIH][hapmap]
rs7976111	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs800166	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs800167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812325	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812326	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs983630	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv525023	chr12:67672870-67708669	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs775310	DYRK2	cis	cerebellum	SCAN
rs775310	CPSF6	cis	cerebellum	SCAN
rs775310	HMGA2	cis	parietal	SCAN
rs775310	AVPR1A	cis	parietal	SCAN
rs775310	YEATS4	cis	cerebellum	SCAN
rs775310	RASSF3	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67664800-67694400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:67664800-67699600	Weak transcription	Aorta	Aorta
3	chr12:67665200-67684400	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:67665200-67684600	Weak transcription	Thymus	Thymus
5	chr12:67665200-67690200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:67665200-67699000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:67665400-67687600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:67666000-67688400	Weak transcription	Fetal Kidney	kidney
9	chr12:67666000-67701000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:67668400-67688200	Weak transcription	HUVEC	blood vessel
11	chr12:67670000-67684200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:67670000-67688800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:67670000-67699200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:67670200-67698200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:67670400-67689600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:67670600-67684400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:67670800-67688400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:67671000-67688800	Weak transcription	NHEK	skin
19	chr12:67671000-67689400	Weak transcription	NHLF	lung
20	chr12:67671200-67688200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:67671400-67698400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:67671600-67691800	Weak transcription	Fetal Brain Male	brain
23	chr12:67672200-67699000	Weak transcription	Esophagus	oesophagus
24	chr12:67672400-67684600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:67672400-67693800	Weak transcription	Psoas Muscle	Psoas
26	chr12:67672600-67684600	Weak transcription	Gastric	stomach
27	chr12:67672600-67684600	Weak transcription	Right Atrium	heart
28	chr12:67673200-67699400	Weak transcription	Small Intestine	intestine
29	chr12:67674200-67684600	Weak transcription	Brain Anterior Caudate	brain
30	chr12:67674200-67688800	Weak transcription	Brain Angular Gyrus	brain
31	chr12:67674200-67694000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:67674400-67684600	Weak transcription	Fetal Lung	lung
33	chr12:67674400-67696000	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:67674600-67689800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:67674600-67708000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:67674800-67697800	Strong transcription	Fetal Thymus	thymus
37	chr12:67674800-67706400	Weak transcription	Stomach Mucosa	stomach
38	chr12:67675400-67685400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:67675600-67685200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:67675600-67694600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:67675800-67685600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:67676200-67691000	Weak transcription	HMEC	breast
43	chr12:67676600-67685000	Strong transcription	A549	lung
44	chr12:67676800-67691800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:67677400-67684600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:67677600-67684400	Weak transcription	Brain Germinal Matrix	brain
47	chr12:67678600-67684200	Weak transcription	Liver	Liver
48	chr12:67678600-67699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:67678800-67684200	Weak transcription	HSMMtube	muscle
50	chr12:67678800-67688400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links