Variant report

Variant	rs644412
Chromosome Location	chr1:179892028-179892029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179890721..179893462-chr1:179922578..179925183,2	MCF-7	breast:
2	chr1:179890847..179892932-chr1:179926143..179929567,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOR1AIP1-3	chr1:179891690-179894128	NONHSAT008230

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1014394	0.81[TSI][hapmap]
rs1144575	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1148812	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1148815	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12062341	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12062383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281378	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281408	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1281411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1281412	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1281413	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281428	0.91[ASN][1000 genomes]
rs1281429	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281430	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281432	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1298477	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1298479	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1300068	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2007148	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245425	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249346	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2762858	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777908	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777909	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777917	0.90[AMR][1000 genomes]
rs2794582	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2794583	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474258	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475233	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475434	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs479094	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs480377	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480498	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486906	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs501300	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502036	0.84[CHD][hapmap]
rs505789	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs505837	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507603	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs514421	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518774	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs522534	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530369	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs530854	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs531814	0.81[CEU][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs538512	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547776	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs549650	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553830	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555526	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs589780	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600046	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600553	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609521	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612215	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657364	0.84[GIH][hapmap]
rs7530362	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs644412	MRPS14	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
2	chr1:179887200-179893400	Weak transcription	Pancreas	Pancrea
3	chr1:179887200-179897200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:179887400-179892800	Weak transcription	Gastric	stomach
5	chr1:179887400-179894600	Weak transcription	HSMMtube	muscle
6	chr1:179887400-179897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:179887400-179897600	Weak transcription	Aorta	Aorta
8	chr1:179887400-179898600	Weak transcription	Right Ventricle	heart
9	chr1:179887400-179899200	Weak transcription	Small Intestine	intestine
10	chr1:179887400-179900600	Weak transcription	Ovary	ovary
11	chr1:179887400-179901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:179887600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:179887600-179899400	Weak transcription	K562	blood
14	chr1:179887800-179892200	Weak transcription	Colonic Mucosa	Colon
15	chr1:179887800-179893000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:179887800-179899400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:179888000-179894600	Weak transcription	HMEC	breast
18	chr1:179888200-179892200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:179888200-179892400	Weak transcription	Fetal Brain Female	brain
20	chr1:179888600-179892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:179888600-179892800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:179888600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:179888600-179895600	Weak transcription	NHLF	lung
24	chr1:179888600-179897200	Weak transcription	Esophagus	oesophagus
25	chr1:179888600-179897200	Weak transcription	Fetal Intestine Large	intestine
26	chr1:179888600-179899400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:179888800-179892400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:179888800-179894400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:179888800-179900600	Weak transcription	Adipose Nuclei	Adipose
30	chr1:179889000-179899400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:179889200-179894200	Weak transcription	Hela-S3	cervix
32	chr1:179889200-179895000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:179889200-179899200	Weak transcription	HepG2	liver
34	chr1:179889400-179892200	Weak transcription	Fetal Thymus	thymus
35	chr1:179889600-179895000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:179889600-179895600	Weak transcription	NHDF-Ad	bronchial
37	chr1:179890200-179892800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:179890200-179895400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:179890400-179892200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:179890400-179892400	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr1:179890400-179892400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:179890400-179892400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:179890400-179892600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr1:179890400-179893000	Weak transcription	Fetal Stomach	stomach
45	chr1:179890800-179893000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:179890800-179893200	Weak transcription	Dnd41	blood
47	chr1:179890800-179893800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:179890800-179894600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:179891000-179892200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:179891000-179892200	Weak transcription	Thymus	Thymus

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