Variant report

Variant	rs1701698
Chromosome Location	chr12:56297625-56297626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10128982	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1052206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747760	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10783774	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783775	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876858	0.86[ASN][1000 genomes]
rs10876861	0.84[ASN][1000 genomes]
rs10876862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171688	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1136082	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12298127	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12320309	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1681070	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1681082	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1701699	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1807168	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2101718	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4414258	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61956428	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581086	0.84[ASN][1000 genomes]
rs6581087	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs705711	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7135133	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7297871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7302957	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7308505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7312870	0.81[EUR][1000 genomes]
rs772461	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs772462	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs772468	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs772473	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs772475	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs772700	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs772704	0.94[CEU][hapmap]
rs7979046	0.87[ASN][1000 genomes]
rs9739192	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739196	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv3347258	chr12:56267734-56298106	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1701698	LARP4	cis	parietal	SCAN
rs1701698	SDR9C7	cis	cerebellum	SCAN
rs1701698	GLS2	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56279800-56320000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56285200-56320000	Weak transcription	Pancreas	Pancrea
3	chr12:56291000-56308400	Weak transcription	Right Atrium	heart
4	chr12:56291400-56319000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:56292000-56298600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:56292600-56298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:56292800-56297800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:56292800-56298000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:56292800-56316000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:56293000-56298000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:56293000-56307800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:56293200-56299800	Weak transcription	HSMMtube	muscle
13	chr12:56293200-56307000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:56293200-56307200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:56293200-56307400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:56293400-56300000	Weak transcription	A549	lung
17	chr12:56293600-56319200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:56293800-56319600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:56294000-56298000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:56294000-56298000	Strong transcription	Fetal Stomach	stomach
21	chr12:56294200-56298000	Strong transcription	Fetal Lung	lung
22	chr12:56294200-56302600	Weak transcription	Brain Anterior Caudate	brain
23	chr12:56294200-56319400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:56294400-56302800	Weak transcription	Stomach Mucosa	stomach
25	chr12:56294400-56313800	Weak transcription	Ovary	ovary
26	chr12:56294400-56319600	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:56294600-56308000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:56295000-56298000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:56295400-56298000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:56296000-56297800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:56296000-56299800	Weak transcription	NHEK	skin
32	chr12:56296000-56301400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:56296000-56307800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:56296000-56319600	Weak transcription	Right Ventricle	heart
35	chr12:56296200-56303000	Weak transcription	Small Intestine	intestine
36	chr12:56296200-56319400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:56296400-56298000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:56296400-56302600	Weak transcription	K562	blood
39	chr12:56296800-56306800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:56296800-56319600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr12:56297000-56315800	Weak transcription	Aorta	Aorta
42	chr12:56297200-56300000	Weak transcription	NHLF	lung
43	chr12:56297200-56301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:56297200-56302800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:56297200-56305400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:56297200-56306200	Weak transcription	Placenta	Placenta
47	chr12:56297200-56306800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:56297200-56306800	Weak transcription	Primary T cells from cord blood	blood
49	chr12:56297200-56306800	Weak transcription	HSMM	muscle
50	chr12:56297200-56307600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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