Variant report

Variant	rs706793
Chromosome Location	chr12:50467769-50467770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:50467700-50467837	H1-hESC	embryonic stem cell:	n/a	chr12:50467719-50467730

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50450302..50454051-chr12:50467339..50469182,3	K562	blood:
2	chr12:50464722..50467382-chr12:50467593..50469329,2	K562	blood:
3	chr12:50465539..50467962-chr12:50472151..50474107,2	K562	blood:
4	chr12:50452539..50455408-chr12:50466138..50467868,2	MCF-7	breast:
5	chr12:50467353..50469226-chr12:50536812..50539286,2	MCF-7	breast:
6	chr12:50467357..50469479-chr12:50676933..50678853,2	K562	blood:
7	chr12:50467506..50470461-chr12:50478607..50480499,2	MCF-7	breast:
8	chr12:50449658..50451557-chr12:50467280..50470251,2	MCF-7	breast:
9	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
10	chr12:50464486..50466222-chr12:50466787..50469329,2	K562	blood:
11	chr12:50360085..50362096-chr12:50467242..50469135,2	K562	blood:
12	chr12:50359952..50361585-chr12:50467635..50470451,2	K562	blood:

No data

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000139624	Chromatin interaction
ENSG00000086159	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000203433	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1044370	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1862043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1979702	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2178173	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2272391	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs2358538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs578470	0.92[EUR][1000 genomes]
rs646782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6580729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs706790	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs706791	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs706792	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7297421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7302981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7308356	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs835592	0.80[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs836170	0.84[EUR][1000 genomes]
rs836171	0.84[EUR][1000 genomes]
rs836172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836173	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836174	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836176	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836179	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs836180	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs836188	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs836189	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs844347	0.96[CEU][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs860698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs706793	MCRS1	cis	parietal	SCAN
rs706793	SNORA2A	cis	parietal	SCAN
rs706793	LASS5	cis	multi-tissue	Pritchard
rs706793	TMEM106C	cis	cerebellum	SCAN
rs706793	SLC38A1	cis	parietal	SCAN
rs706793	LASS5	cis	cerebellum	SCAN
rs706793	CERS5	cis	Nerve Tibial	GTEx
rs706793	LASS5	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50460600-50469200	Weak transcription	Psoas Muscle	Psoas
3	chr12:50460600-50469400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50460800-50469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:50461000-50468800	Weak transcription	HSMMtube	muscle
6	chr12:50464400-50468800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:50464400-50469200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:50464400-50469200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:50464400-50469200	Weak transcription	Fetal Lung	lung
10	chr12:50464400-50469200	Weak transcription	Pancreas	Pancrea
11	chr12:50464400-50478200	Weak transcription	Fetal Heart	heart
12	chr12:50464400-50478200	Weak transcription	Right Atrium	heart
13	chr12:50464600-50468800	Weak transcription	Liver	Liver
14	chr12:50464600-50469200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:50464600-50469600	Weak transcription	Colonic Mucosa	Colon
16	chr12:50464800-50468600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:50464800-50468600	Weak transcription	Fetal Intestine Large	intestine
18	chr12:50464800-50468800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:50464800-50468800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:50464800-50468800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:50464800-50468800	Weak transcription	Fetal Intestine Small	intestine
22	chr12:50464800-50468800	Weak transcription	Gastric	stomach
23	chr12:50464800-50468800	Weak transcription	Right Ventricle	heart
24	chr12:50464800-50468800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:50464800-50468800	Weak transcription	NH-A	brain
26	chr12:50464800-50469000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:50464800-50469000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:50464800-50469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:50464800-50469000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:50464800-50469000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:50464800-50469000	Weak transcription	Stomach Mucosa	stomach
32	chr12:50464800-50469200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:50464800-50469200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:50464800-50469200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:50464800-50469200	Weak transcription	Brain Angular Gyrus	brain
36	chr12:50464800-50469200	Weak transcription	Brain Anterior Caudate	brain
37	chr12:50464800-50469200	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:50464800-50469200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:50464800-50469200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:50464800-50469200	Weak transcription	HMEC	breast
41	chr12:50464800-50471600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:50464800-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:50464800-50478200	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:50464800-50478200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:50464800-50478200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr12:50464800-50478400	Weak transcription	Primary T cells from cord blood	blood
47	chr12:50465000-50468800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:50465000-50468800	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:50465000-50468800	Weak transcription	A549	lung
50	chr12:50465000-50468800	Weak transcription	Dnd41	blood

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