Variant report

Variant	rs1701704
Chromosome Location	chr12:56412487-56412488
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56409853..56412633-chr12:56413115..56416676,5	K562	blood:
2	chr12:56410866..56413481-chr12:56435830..56438234,2	K562	blood:
3	chr12:56395394..56397678-chr12:56412069..56414982,2	MCF-7	breast:
4	chr12:56389168..56393063-chr12:56410604..56414258,3	K562	blood:
5	chr12:56410922..56412613-chr12:56435767..56437391,2	MCF-7	breast:
6	chr12:56404010..56405727-chr12:56409399..56413302,3	MCF-7	breast:
7	chr12:56400079..56406275-chr12:56406695..56413732,8	MCF-7	breast:
8	chr12:56410592..56413106-chr5:6632207..6633783,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000145545	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000037474	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123411	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10876864	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10876866	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876870	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs11171739	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1131017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1689510	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1702877	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1873914	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2017445	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271194	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2292239	0.86[CEU][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2456973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2640562	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2640564	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34415530	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3741499	0.86[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs4759229	0.86[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs61938962	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61938963	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs705696	0.81[EUR][1000 genomes]
rs705698	0.91[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs705699	0.84[CHB][hapmap]
rs705700	0.82[JPT][hapmap]
rs705702	0.91[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs705704	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs705705	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7302200	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7305461	0.81[CHB][hapmap]
rs772920	0.81[EUR][1000 genomes]
rs772921	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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs773107	0.86[CEU][hapmap];0.92[TSI][hapmap]
rs773108	0.90[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap]
rs773109	0.91[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap]
rs773110	0.80[AMR][1000 genomes]
rs773114	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7971751	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs877636	0.86[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.87[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

Variant related diseases (count:4)

Disease	PMID	Source
Type 1 diabetes	18198356	GWAS catalog
Asthma	21804548	GWAS catalog
Type 1 diabetes autoantibodies	21829393	GWAS catalog
Alopecia areata	20596022	GWAS catalog

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1701704	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs1701704	RPS26	cis	multi-tissue	Pritchard
rs1701704	AC034102.1	cis	Muscle Skeletal	GTEx
rs1701704	CSRNP2	cis	parietal	SCAN
rs1701704	DNAJC14	cis	parietal	SCAN
rs1701704	TAC3	cis	parietal	SCAN
rs1701704	RPS26	cis	lymphoblastoid	seeQTL
rs1701704	SUOX	cis	cerebellum	SCAN
rs1701704	DEFB124	trans	lymphoblastoid	RTeQTL
rs1701704	SUOX	cis	parietal	SCAN
rs1701704	KRT82	cis	parietal	SCAN
rs1701704	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs1701704	SUOX	cis	Thyroid	GTEx
rs1701704	MYL6B	cis	cerebellum	SCAN
rs1701704	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs1701704	SMARCC2	cis	parietal	SCAN
rs1701704	RAB5B	cis	Muscle Skeletal	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56402000-56418600	Weak transcription	Gastric	stomach
2	chr12:56402200-56412600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:56402200-56413200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:56402200-56413400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:56402200-56413800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:56402200-56413800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:56402200-56414000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:56402200-56414000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:56402200-56414200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:56402200-56414200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:56402200-56414400	Weak transcription	Primary B cells from cord blood	blood
12	chr12:56402200-56414400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:56402200-56414400	Weak transcription	Brain Angular Gyrus	brain
14	chr12:56402200-56414400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:56402200-56414400	Weak transcription	Left Ventricle	heart
16	chr12:56402200-56414400	Weak transcription	Right Ventricle	heart
17	chr12:56402200-56414400	Weak transcription	Spleen	Spleen
18	chr12:56402200-56414600	Weak transcription	Thymus	Thymus
19	chr12:56402200-56415000	Weak transcription	Lung	lung
20	chr12:56402200-56415200	Weak transcription	NH-A	brain
21	chr12:56402200-56418400	Weak transcription	Pancreas	Pancrea
22	chr12:56402200-56418400	Weak transcription	HSMMtube	muscle
23	chr12:56402200-56434800	Weak transcription	Psoas Muscle	Psoas
24	chr12:56402400-56413200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:56402400-56413400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:56402400-56413400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:56402400-56413400	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:56402400-56413600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:56402400-56413600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:56402400-56413600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:56402400-56413600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:56402400-56413600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:56402400-56413600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:56402400-56413600	Weak transcription	Fetal Brain Male	brain
35	chr12:56402400-56413800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:56402400-56413800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:56402400-56414000	Weak transcription	Primary T cells from cord blood	blood
38	chr12:56402400-56414000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:56402400-56414000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:56402400-56414000	Weak transcription	NHLF	lung
41	chr12:56402400-56414200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:56402400-56414400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:56402400-56414400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:56402400-56414400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:56402400-56414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr12:56402400-56414800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:56402400-56415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:56402400-56422400	Weak transcription	Osteobl	bone
49	chr12:56402400-56423000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:56403000-56414600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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