Variant report

Variant	rs2970808
Chromosome Location	chr12:4640362-4640363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:4638037..4640518-chr12:4647266..4649269,3	K562	blood:
2	chr12:4639152..4642726-chr12:4646208..4648490,3	MCF-7	breast:
3	chr12:4630575..4632650-chr12:4639446..4641631,2	K562	blood:

Variant related genes	Relation type
ENSG00000047621	Chromatin interaction
ENSG00000111247	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1029769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444478	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs10849083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849087	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs10849089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849090	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849091	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11063177	0.84[EUR][1000 genomes]
rs11063179	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11063181	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11063182	0.99[EUR][1000 genomes]
rs11063187	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063188	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063189	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11063191	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11063193	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063194	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063195	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063196	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063197	1.00[ASN][1000 genomes]
rs11063198	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11063199	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063202	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063206	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063213	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063214	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063217	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063220	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11063227	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11063228	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11063230	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12314323	0.91[ASN][1000 genomes]
rs12366731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367035	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907492	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2907494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970812	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970818	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4238020	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4323977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60388479	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61909580	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71459910	0.81[ASN][1000 genomes]
rs73037770	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308641	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs7314915	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7965755	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs7972086	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9971700	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9971728	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2970808	SCARNA10	cis	parietal	SCAN
rs2970808	DYRK4	cis	cerebellum	SCAN
rs2970808	AKAP3	cis	cerebellum	SCAN
rs2970808	C12orf4	cis	brain	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4592400-4647200	Weak transcription	Esophagus	oesophagus
2	chr12:4594400-4646400	Weak transcription	NHLF	lung
3	chr12:4594800-4647000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:4596000-4647200	Weak transcription	Small Intestine	intestine
5	chr12:4596600-4640400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:4598200-4647000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:4598400-4646800	Weak transcription	Fetal Brain Male	brain
8	chr12:4599200-4647200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:4606200-4647200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:4608200-4647200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:4609600-4640400	Weak transcription	Fetal Kidney	kidney
12	chr12:4609600-4642400	Weak transcription	Brain Substantia Nigra	brain
13	chr12:4609800-4640800	Weak transcription	Fetal Brain Female	brain
14	chr12:4610800-4647200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:4611200-4647000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:4615000-4642200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:4615000-4646400	Weak transcription	Fetal Heart	heart
18	chr12:4616400-4640600	Weak transcription	HSMMtube	muscle
19	chr12:4616400-4646000	Weak transcription	HepG2	liver
20	chr12:4617000-4646600	Weak transcription	NHEK	skin
21	chr12:4624400-4645400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:4624400-4646400	Weak transcription	K562	blood
23	chr12:4626400-4640800	Weak transcription	Pancreas	Pancrea
24	chr12:4626400-4641000	Weak transcription	Psoas Muscle	Psoas
25	chr12:4627600-4640400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:4627600-4645600	Weak transcription	HMEC	breast
27	chr12:4627600-4646600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:4629000-4641400	Weak transcription	Right Ventricle	heart
29	chr12:4629200-4647000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:4629600-4640800	Weak transcription	Lung	lung
31	chr12:4629600-4642400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:4629600-4647000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:4629600-4647200	Weak transcription	Gastric	stomach
34	chr12:4629800-4640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:4629800-4640600	Weak transcription	Spleen	Spleen
36	chr12:4629800-4640800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:4629800-4646600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:4629800-4647000	Weak transcription	Fetal Intestine Small	intestine
39	chr12:4630000-4640400	Weak transcription	Thymus	Thymus
40	chr12:4630000-4640600	Weak transcription	Fetal Stomach	stomach
41	chr12:4630000-4640600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:4630000-4645400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:4630000-4646400	Weak transcription	Brain Germinal Matrix	brain
44	chr12:4631600-4644600	Strong transcription	Dnd41	blood
45	chr12:4631800-4640800	Weak transcription	Ovary	ovary
46	chr12:4633600-4642400	Weak transcription	A549	lung
47	chr12:4634000-4640400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:4634000-4641000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:4634000-4642400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:4634200-4642400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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