Variant report

Variant	rs706791
Chromosome Location	chr12:50465355-50465356
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50465226..50467523-chr12:50469793..50471990,2	K562	blood:
2	chr12:50464486..50466222-chr12:50466787..50469329,2	K562	blood:
3	chr12:50259278..50261065-chr12:50464788..50467159,2	K562	blood:
4	chr12:50464456..50466840-chr12:50477683..50480596,2	MCF-7	breast:
5	chr12:50464941..50466532-chr12:50496358..50498847,2	MCF-7	breast:
6	chr12:50360634..50361442-chr12:50465226..50466043,2	K562	blood:
7	chr12:50452088..50458692-chr12:50460164..50465883,8	K562	blood:
8	chr12:50450859..50453547-chr12:50463168..50465511,2	MCF-7	breast:
9	chr12:50359856..50363195-chr12:50464299..50467277,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000086159	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000167588	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1044370	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1862043	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1979702	0.89[CEU][hapmap];0.93[GIH][hapmap];0.88[EUR][1000 genomes]
rs2178173	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2272391	0.92[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs2358538	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs578470	0.92[EUR][1000 genomes]
rs646782	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6580729	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs706790	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs706792	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][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]
rs706793	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]
rs7136570	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs7279	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap]
rs7297421	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs7302981	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs7308356	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs7532	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap]
rs835592	0.92[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs836170	0.83[EUR][1000 genomes]
rs836171	0.83[EUR][1000 genomes]
rs836172	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836173	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836174	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836176	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs836179	1.00[CHB][hapmap]
rs836180	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs836188	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs836189	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs844347	0.92[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs860698	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.98[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs706791	LASS5	cis	parietal	SCAN
rs706791	TMEM106C	cis	cerebellum	SCAN
rs706791	CERS5	cis	Nerve Tibial	GTEx
rs706791	LASS5	cis	cerebellum	SCAN
rs706791	SNORA2A	cis	parietal	SCAN
rs706791	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50460600-50465800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:50460600-50466000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:50460600-50469200	Weak transcription	Psoas Muscle	Psoas
5	chr12:50460600-50469400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:50460800-50469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:50461000-50465600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:50461000-50468800	Weak transcription	HSMMtube	muscle
9	chr12:50464000-50467000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:50464400-50465600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:50464400-50465800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:50464400-50465800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:50464400-50466800	Weak transcription	Fetal Kidney	kidney
14	chr12:50464400-50467400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:50464400-50467600	Weak transcription	HepG2	liver
16	chr12:50464400-50468800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:50464400-50469200	Weak transcription	Brain Substantia Nigra	brain
18	chr12:50464400-50469200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:50464400-50469200	Weak transcription	Fetal Lung	lung
20	chr12:50464400-50469200	Weak transcription	Pancreas	Pancrea
21	chr12:50464400-50478200	Weak transcription	Fetal Heart	heart
22	chr12:50464400-50478200	Weak transcription	Right Atrium	heart
23	chr12:50464600-50465600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:50464600-50467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:50464600-50468800	Weak transcription	Liver	Liver
26	chr12:50464600-50469200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:50464600-50469600	Weak transcription	Colonic Mucosa	Colon
28	chr12:50464800-50465400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:50464800-50465600	Weak transcription	Fetal Stomach	stomach
30	chr12:50464800-50465800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:50464800-50465800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:50464800-50465800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:50464800-50465800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:50464800-50465800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:50464800-50466000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:50464800-50466000	Weak transcription	Brain Germinal Matrix	brain
37	chr12:50464800-50466400	Weak transcription	Fetal Brain Male	brain
38	chr12:50464800-50466800	Enhancers	K562	blood
39	chr12:50464800-50468600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:50464800-50468600	Weak transcription	Fetal Intestine Large	intestine
41	chr12:50464800-50468800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:50464800-50468800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:50464800-50468800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:50464800-50468800	Weak transcription	Fetal Intestine Small	intestine
45	chr12:50464800-50468800	Weak transcription	Gastric	stomach
46	chr12:50464800-50468800	Weak transcription	Right Ventricle	heart
47	chr12:50464800-50468800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:50464800-50468800	Weak transcription	NH-A	brain
49	chr12:50464800-50469000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:50464800-50469000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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