Variant report

Variant	rs1628766
Chromosome Location	chr12:12250849-12250850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12242492..12245826-chr12:12250715..12252862,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1612841	0.95[CEU][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs1615942	0.84[CHD][hapmap]
rs1630467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641727	0.95[CEU][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs1641728	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]
rs1641729	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1797646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1797662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2111166	0.82[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs2160523	0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs2430610	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2430611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2430612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448029	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2448030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2448049	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2448051	0.83[CHD][hapmap]
rs2448052	0.84[CHD][hapmap]
rs2961550	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2961551	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2961552	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2961553	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2961554	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851594	0.80[ASN][1000 genomes]
rs885636	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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
rs1628766	KLRC1	cis	parietal	SCAN
rs1628766	KLRA1	cis	cerebellum	SCAN
rs1628766	PRR4	cis	parietal	SCAN

Chromatin state (count:73 , 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	chr12:12240400-12254200	Weak transcription	Stomach Mucosa	stomach
9	chr12:12240600-12256800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:12241000-12260600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:12241000-12273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:12241200-12256800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:12241200-12261000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:12241400-12252000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:12241400-12272600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:12241800-12260400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:12242000-12251000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:12242000-12257000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:12245600-12251000	Weak transcription	Placenta	Placenta
20	chr12:12245600-12251000	Weak transcription	Left Ventricle	heart
21	chr12:12245600-12252000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:12245600-12253600	Weak transcription	Colonic Mucosa	Colon
23	chr12:12245600-12257000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:12245600-12260400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:12245600-12260400	Weak transcription	Fetal Brain Female	brain
26	chr12:12245600-12260600	Weak transcription	Psoas Muscle	Psoas
27	chr12:12245800-12251600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:12245800-12252000	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:12245800-12255600	Weak transcription	Brain Substantia Nigra	brain
30	chr12:12245800-12256600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:12245800-12256600	Weak transcription	Lung	lung
32	chr12:12245800-12260400	Weak transcription	Brain Germinal Matrix	brain
33	chr12:12245800-12260400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:12245800-12260600	Weak transcription	Brain Hippocampus Middle	brain
35	chr12:12245800-12263800	Weak transcription	Pancreas	Pancrea
36	chr12:12245800-12266200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:12246000-12254400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:12246000-12256600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:12246200-12251800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:12246200-12253600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:12246200-12253600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:12246200-12256000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:12246200-12260400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:12246200-12260400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:12246400-12251000	Weak transcription	Liver	Liver
46	chr12:12246400-12251800	Weak transcription	A549	lung
47	chr12:12246400-12257000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:12246400-12272000	Weak transcription	Osteobl	bone
49	chr12:12247600-12261400	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:12247800-12251000	Weak transcription	Right Atrium	heart

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