Variant report

Variant	rs1667583
Chromosome Location	chr12:122370206-122370207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr12:122370059-122370226	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr12:122369911-122370206	SH-SY5Y	brain:	n/a	n/a
3	CBX3	chr12:122370024-122370491	K562	blood:	n/a	n/a
4	TBL1XR1	chr12:122370148-122370264	K562	blood:	n/a	n/a
5	ZNF143	chr12:122370089-122370316	K562	blood:	n/a	n/a
6	RCOR1	chr12:122370064-122370379	K562	blood:	n/a	n/a
7	RCOR1	chr12:122370068-122370422	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122355684..122357967-chr12:122369270..122371880,2	K562	blood:
2	chr12:122353628..122357829-chr12:122368964..122373628,4	MCF-7	breast:
3	chr12:122369123..122373485-chr12:122458454..122462950,5	K562	blood:
4	chr12:122366441..122369045-chr12:122369875..122372050,2	K562	blood:
5	chr12:122355624..122357967-chr12:122370172..122371880,2	K562	blood:

No data

Variant related genes	Relation type
WDR66	TF binding region
ENSG00000110987	Chromatin interaction
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10840626	0.82[EUR][1000 genomes]
rs10840627	0.85[EUR][1000 genomes]
rs11043222	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11043248	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs1154510	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1154513	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1154515	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11614623	0.85[EUR][1000 genomes]
rs1169075	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1169077	0.82[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1169080	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169082	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1169085	0.82[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1169092	0.89[ASN][1000 genomes]
rs1169093	0.82[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[ASN][1000 genomes]
rs1182927	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1185260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1667580	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1667584	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678951	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678967	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678969	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720041	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs1720067	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1795967	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1916333	0.90[ASN][1000 genomes]
rs1947826	0.81[EUR][1000 genomes]
rs2101017	0.81[EUR][1000 genomes]
rs2230681	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2247139	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247291	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap]
rs2309274	0.81[EUR][1000 genomes]
rs2596137	0.81[EUR][1000 genomes]
rs2596144	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2620332	0.81[EUR][1000 genomes]
rs2620340	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2620353	0.86[ASN][1000 genomes]
rs2688412	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2707056	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4760099	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs493519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs529736	0.86[MEX][hapmap]
rs6486794	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap]
rs693277	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314056	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7957207	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap]
rs7961103	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap]
rs830116	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830120	0.81[MEX][hapmap]
rs830122	0.82[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830123	0.90[MEX][hapmap]
rs830124	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap]
rs830126	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs853758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs895958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895959	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9668191	0.91[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1667583	CCDC62	cis	parietal	SCAN
rs1667583	SETD1B	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122357000-122370600	Weak transcription	Aorta	Aorta
2	chr12:122357000-122380400	Weak transcription	Gastric	stomach
3	chr12:122357000-122383600	Weak transcription	Primary T cells from cord blood	blood
4	chr12:122363000-122384800	Weak transcription	Psoas Muscle	Psoas
5	chr12:122363000-122393400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:122363200-122384600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:122363400-122372000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:122363400-122375000	Weak transcription	Spleen	Spleen
9	chr12:122363400-122377000	Weak transcription	Fetal Intestine Small	intestine
10	chr12:122363600-122370400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:122363600-122371600	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:122363600-122374400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:122363600-122374400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:122363600-122374600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:122363600-122375000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:122363600-122375000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:122363600-122375400	Weak transcription	Right Atrium	heart
18	chr12:122363600-122377400	Weak transcription	Fetal Brain Female	brain
19	chr12:122363600-122383600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:122363600-122383800	Weak transcription	Fetal Brain Male	brain
21	chr12:122363600-122385600	Weak transcription	Fetal Lung	lung
22	chr12:122363600-122392200	Weak transcription	Left Ventricle	heart
23	chr12:122363600-122398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
25	chr12:122363800-122371000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:122364400-122372000	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:122365400-122375000	Weak transcription	Lung	lung
28	chr12:122365600-122370600	Weak transcription	Pancreas	Pancrea
29	chr12:122365600-122385800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:122365600-122393400	Weak transcription	Brain Substantia Nigra	brain
31	chr12:122365800-122370600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:122365800-122371200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:122365800-122371200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:122365800-122371200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:122365800-122371600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:122365800-122374600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:122365800-122375000	Weak transcription	Liver	Liver
38	chr12:122365800-122390200	Weak transcription	HUVEC	blood vessel
39	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr12:122366000-122370600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:122366000-122370800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:122366000-122371000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:122366000-122371000	Weak transcription	A549	lung
44	chr12:122366000-122371200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:122366000-122371200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:122366000-122371200	Weak transcription	Fetal Thymus	thymus
47	chr12:122366000-122371400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:122366000-122371400	Weak transcription	NH-A	brain
49	chr12:122366000-122372000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:122366000-122372000	Weak transcription	NHLF	lung

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