Variant report

Variant	rs1641728
Chromosome Location	chr12:12247360-12247361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1612841	0.95[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1615942	0.84[CHD][hapmap]
rs1628766	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1630467	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1641727	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1641729	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1797646	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1797647	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1797662	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2111166	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs2160523	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs2430610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2430611	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2430612	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2448029	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2448030	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2448031	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2448048	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2448049	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2448051	0.83[CHD][hapmap]
rs2448052	0.84[CHD][hapmap]
rs2448053	0.88[MKK][hapmap]
rs2961550	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2961551	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2961552	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2961553	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2961554	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851594	0.86[ASN][1000 genomes]
rs885636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv557583	chr12:12238317-12253591	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1641728	PRR4	cis	parietal	SCAN
rs1641728	KLRC1	cis	parietal	SCAN
rs1641728	KLRA1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12225000-12255000	Weak transcription	Small Intestine	intestine
2	chr12:12232800-12257000	Weak transcription	HSMMtube	muscle
3	chr12:12234800-12259600	Weak transcription	Aorta	Aorta
4	chr12:12235400-12260200	Weak transcription	Gastric	stomach
5	chr12:12235400-12260800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:12235400-12278800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:12237400-12259800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:12239600-12249200	Strong transcription	Fetal Intestine Small	intestine
9	chr12:12240400-12254200	Weak transcription	Stomach Mucosa	stomach
10	chr12:12240600-12256800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:12241000-12250200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:12241000-12260600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:12241000-12273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:12241200-12256800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:12241200-12261000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:12241400-12252000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:12241400-12272600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:12241800-12247400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:12241800-12260400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:12242000-12251000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:12242000-12257000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:12242800-12249000	Strong transcription	Fetal Intestine Large	intestine
23	chr12:12245200-12247400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:12245600-12251000	Weak transcription	Placenta	Placenta
25	chr12:12245600-12251000	Weak transcription	Left Ventricle	heart
26	chr12:12245600-12252000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:12245600-12253600	Weak transcription	Colonic Mucosa	Colon
28	chr12:12245600-12257000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:12245600-12260400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:12245600-12260400	Weak transcription	Fetal Brain Female	brain
31	chr12:12245600-12260600	Weak transcription	Psoas Muscle	Psoas
32	chr12:12245800-12248400	Weak transcription	Fetal Stomach	stomach
33	chr12:12245800-12251600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:12245800-12252000	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:12245800-12255600	Weak transcription	Brain Substantia Nigra	brain
36	chr12:12245800-12256600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:12245800-12256600	Weak transcription	Lung	lung
38	chr12:12245800-12260400	Weak transcription	Brain Germinal Matrix	brain
39	chr12:12245800-12260400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr12:12245800-12260600	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:12245800-12263800	Weak transcription	Pancreas	Pancrea
42	chr12:12245800-12266200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:12246000-12247800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:12246000-12254400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:12246000-12256600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:12246200-12247400	Weak transcription	Fetal Lung	lung
47	chr12:12246200-12248000	Weak transcription	Hela-S3	cervix
48	chr12:12246200-12251800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:12246200-12253600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:12246200-12253600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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