Variant report

Variant	rs7965755
Chromosome Location	chr12:4669740-4669741
allele	G/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	POLR2A	chr12:4669684-4669813	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:4669691-4670598	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:4669346-4670585	K562	blood:	n/a	n/a
4	POLR2A	chr12:4669713-4669764	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:4669594-4670600	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4666221..4667808-chr12:4669530..4671066,2	K562	blood:
2	chr12:4664388..4668244-chr12:4668539..4671250,3	K562	blood:

Variant related genes	Relation type
DYRK4	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1029769	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10444478	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10849083	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10849085	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10849086	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs10849087	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849089	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10849090	0.91[ASN][1000 genomes]
rs10849091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11063187	0.91[ASN][1000 genomes]
rs11063188	0.91[ASN][1000 genomes]
rs11063193	0.91[ASN][1000 genomes]
rs11063194	0.91[ASN][1000 genomes]
rs11063195	0.91[ASN][1000 genomes]
rs11063196	0.91[ASN][1000 genomes]
rs11063197	0.91[ASN][1000 genomes]
rs11063199	0.91[ASN][1000 genomes]
rs11063202	0.91[ASN][1000 genomes]
rs11063205	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs11063206	0.91[ASN][1000 genomes]
rs11063207	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs11063213	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11063214	0.91[ASN][1000 genomes]
rs11063215	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11063217	0.91[ASN][1000 genomes]
rs11063220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11063227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063230	1.00[CHB][hapmap];0.85[GIH][hapmap];0.91[ASN][1000 genomes]
rs12314323	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366731	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12367035	0.91[ASN][1000 genomes]
rs2907492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907494	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs2907495	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2907498	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2907499	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2909380	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2909381	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2970808	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs2970810	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2970812	0.91[ASN][1000 genomes]
rs2970818	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4238020	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4323977	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs60388479	0.91[ASN][1000 genomes]
rs61909580	0.91[ASN][1000 genomes]
rs71459910	0.91[ASN][1000 genomes]
rs73037770	0.91[ASN][1000 genomes]
rs7304949	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7308641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9971700	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9971728	0.91[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	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1038332	chr12:4627992-4689300	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541362	chr12:4627992-4689300	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7965755	SCARNA10	cis	parietal	SCAN
rs7965755	LAG3	cis	parietal	SCAN
rs7965755	LEPREL2	cis	parietal	SCAN
rs7965755	SCARNA12	cis	parietal	SCAN
rs7965755	DYRK4	cis	cerebellum	SCAN
rs7965755	FBXL14	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4648400-4670200	Weak transcription	Left Ventricle	heart
2	chr12:4648400-4671200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:4648400-4671400	Weak transcription	Esophagus	oesophagus
4	chr12:4648600-4671200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:4648800-4670800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:4648800-4671000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:4649000-4671000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:4649000-4671000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:4649000-4671000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:4649000-4671200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:4649200-4670800	Weak transcription	Fetal Intestine Small	intestine
12	chr12:4649400-4671000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:4649400-4671000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:4649400-4671000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:4649600-4671000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:4649600-4671000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:4649600-4671000	Weak transcription	Fetal Kidney	kidney
18	chr12:4649600-4671200	Weak transcription	NHEK	skin
19	chr12:4650200-4670600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:4650400-4670000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:4650400-4670200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:4651000-4670400	Strong transcription	Fetal Thymus	thymus
23	chr12:4652000-4671800	Strong transcription	Dnd41	blood
24	chr12:4654400-4671000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:4655400-4671000	Weak transcription	NH-A	brain
26	chr12:4655600-4671000	Weak transcription	Osteobl	bone
27	chr12:4657000-4671000	Weak transcription	NHDF-Ad	bronchial
28	chr12:4657800-4671000	Weak transcription	Fetal Intestine Large	intestine
29	chr12:4658000-4671000	Weak transcription	Fetal Heart	heart
30	chr12:4658400-4671600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:4659000-4671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:4659200-4670000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:4659400-4670200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:4659400-4671200	Weak transcription	Primary T cells from cord blood	blood
35	chr12:4659800-4671000	Weak transcription	Brain Germinal Matrix	brain
36	chr12:4659800-4671000	Weak transcription	K562	blood
37	chr12:4660000-4671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:4660000-4671400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:4660200-4671000	Weak transcription	HepG2	liver
40	chr12:4660200-4671000	Weak transcription	HUVEC	blood vessel
41	chr12:4661800-4670400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:4662000-4671000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:4663400-4671200	Weak transcription	Psoas Muscle	Psoas
44	chr12:4664600-4671000	Weak transcription	Spleen	Spleen
45	chr12:4665000-4671000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:4665000-4671000	Weak transcription	Fetal Lung	lung
47	chr12:4666200-4671000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:4666200-4671000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:4666400-4671000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:4666400-4671200	Weak transcription	Aorta	Aorta

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