Variant report

Variant	rs2290893
Chromosome Location	chr12:57078620-57078621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57078051..57079984-chr12:57144194..57146255,2	MCF-7	breast:
2	chr12:57071098..57073439-chr12:57077293..57080257,6	MCF-7	breast:
3	chr12:57057109..57062087-chr12:57076163..57079993,5	MCF-7	breast:
4	chr12:57075341..57085478-chr12:57112447..57121011,58	MCF-7	breast:
5	chr12:57076071..57078890-chr12:57104142..57106874,2	K562	blood:
6	chr12:57078475..57085183-chr12:57112918..57121559,38	K562	blood:
7	chr12:57035919..57041993-chr12:57078486..57083961,15	MCF-7	breast:
8	chr12:57038667..57042033-chr12:57076746..57080417,4	K562	blood:
9	chr12:57077883..57080577-chr12:57094681..57096906,2	K562	blood:
10	chr12:57078269..57080513-chr12:57145758..57148526,2	K562	blood:
11	chr12:57037416..57042033-chr12:57076746..57084678,17	K562	blood:
12	chr12:57078008..57083064-chr12:57107591..57112002,6	MCF-7	breast:
13	chr12:57074578..57085543-chr12:57108746..57121559,55	K562	blood:
14	chr12:57076604..57085974-chr12:57112559..57120474,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110955	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000207031	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1020848	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1026565	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs10450	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs10747769	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783794	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs10783796	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10876913	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876914	0.92[ASN][1000 genomes]
rs10876915	0.92[ASN][1000 genomes]
rs10876916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876918	0.81[AMR][1000 genomes]
rs1107479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171914	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171916	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171917	0.92[ASN][1000 genomes]
rs11171951	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11171956	0.83[EUR][1000 genomes]
rs1131514	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11835120	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11837319	0.92[ASN][1000 genomes]
rs12229457	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12828563	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1465081	0.92[ASN][1000 genomes]
rs1466382	0.83[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1563896	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1563897	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1962963	0.81[ASN][1000 genomes]
rs1975875	0.81[EUR][1000 genomes]
rs1979325	0.93[CHB][hapmap]
rs2035081	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2035082	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2242497	0.85[YRI][hapmap]
rs2255074	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290894	0.95[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2926740	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2926741	0.95[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes]
rs2926743	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2926747	0.83[EUR][1000 genomes]
rs2926748	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2950387	0.87[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs2950388	0.92[ASN][1000 genomes]
rs2950389	0.90[JPT][hapmap]
rs2950390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2950393	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2950394	0.92[ASN][1000 genomes]
rs2958123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2958124	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2958127	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2958130	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs2958145	0.92[ASN][1000 genomes]
rs2958146	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2958148	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs2958149	0.87[CHB][hapmap]
rs2958153	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2958154	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2958155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3214051	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs36012661	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4759028	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759254	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67046307	0.92[ASN][1000 genomes]
rs7295862	1.00[CEU][hapmap]
rs7297289	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303216	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309526	0.84[ASN][1000 genomes]
rs7313074	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7315472	0.92[ASN][1000 genomes]
rs73337030	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957300	0.89[EUR][1000 genomes]
rs7966391	0.81[EUR][1000 genomes]
rs7967600	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap]
rs7972420	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7973157	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7975783	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978685	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7980317	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap]
rs7980378	0.94[ASN][1000 genomes]
rs7980835	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898609	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs898611	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs9368	0.81[CHB][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap]
rs941207	0.93[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs941209	0.84[JPT][hapmap]
rs9634246	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9634247	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9634277	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9989034	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2290893	RAB5B	cis	cerebellum	SCAN
rs2290893	IL23A	cis	cerebellum	SCAN
rs2290893	PRIM1	cis	parietal	SCAN
rs2290893	HOXC6	cis	cerebellum	SCAN
rs2290893	CELA1	cis	cerebellum	SCAN
rs2290893	PRIM1	cis	cerebellum	SCAN
rs2290893	STAT6	cis	parietal	SCAN
rs2290893	OR10A7	cis	parietal	SCAN
rs2290893	HSD17B6	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57065200-57079800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:57073000-57080200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:57074800-57079600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:57074800-57079600	Weak transcription	Esophagus	oesophagus
5	chr12:57076200-57079000	Weak transcription	Gastric	stomach
6	chr12:57076400-57078800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:57076600-57079400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:57077000-57080400	Active TSS	HepG2	liver
9	chr12:57077000-57081000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr12:57077000-57083800	Active TSS	GM12878-XiMat	blood
11	chr12:57077200-57078800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:57077200-57079600	Weak transcription	Spleen	Spleen
13	chr12:57077200-57083400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:57077400-57078800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:57077400-57078800	Active TSS	Fetal Intestine Small	intestine
16	chr12:57077400-57079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:57077400-57080200	Weak transcription	Lung	lung
18	chr12:57077400-57083200	Active TSS	Colonic Mucosa	Colon
19	chr12:57077600-57078800	Active TSS	Fetal Intestine Large	intestine
20	chr12:57077600-57079000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr12:57077600-57079200	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr12:57077600-57079200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:57077800-57078800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
24	chr12:57077800-57078800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr12:57077800-57078800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:57077800-57078800	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr12:57077800-57078800	Flanking Active TSS	HUVEC	blood vessel
28	chr12:57077800-57078800	Flanking Active TSS	NHEK	skin
29	chr12:57077800-57079000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:57077800-57079000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
31	chr12:57077800-57079000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
32	chr12:57077800-57079000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr12:57077800-57079000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:57077800-57079000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr12:57077800-57079000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr12:57077800-57079000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:57077800-57079000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
38	chr12:57077800-57079000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr12:57077800-57079000	Active TSS	Colon Smooth Muscle	Colon
40	chr12:57077800-57079000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr12:57077800-57079000	Enhancers	Fetal Heart	heart
42	chr12:57077800-57079000	Transcr. at gene 5' and 3'	A549	lung
43	chr12:57077800-57079200	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr12:57077800-57079200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:57077800-57079200	Flanking Active TSS	Osteobl	bone
46	chr12:57077800-57079400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:57077800-57079600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:57077800-57079600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:57077800-57079800	Active TSS	NHDF-Ad	bronchial
50	chr12:57077800-57080600	Enhancers	Fetal Brain Male	brain

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