Variant report

Variant	rs1146648
Chromosome Location	chr1:76265890-76265891
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76259028..76263655-chr1:76264104..76269438,8	MCF-7	breast:
2	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
3	chr1:76263795..76266043-chr1:76279563..76282282,3	K562	blood:
4	chr1:76256951..76259579-chr1:76264447..76268125,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057468	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 165 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs1021462	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10732724	0.85[JPT][hapmap]
rs10782556	0.82[ASN][1000 genomes]
rs10873724	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873727	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873728	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873735	0.82[ASN][1000 genomes]
rs10873738	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10873739	0.99[ASN][1000 genomes]
rs10873804	0.81[JPT][hapmap]
rs1093006	0.80[ASN][1000 genomes]
rs1093009	0.80[ASN][1000 genomes]
rs11161447	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11161465	0.86[JPT][hapmap]
rs11161602	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11161700	0.99[ASN][1000 genomes]
rs11161704	0.95[ASN][1000 genomes]
rs11161731	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11161790	0.90[ASN][1000 genomes]
rs11161795	0.90[ASN][1000 genomes]
rs11161852	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11161887	0.85[JPT][hapmap]
rs1144328	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs1144331	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1144333	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1144337	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1144338	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1144339	0.95[ASN][1000 genomes]
rs1144341	0.95[ASN][1000 genomes]
rs1144342	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1146572	0.81[ASN][1000 genomes]
rs1146592	0.84[ASN][1000 genomes]
rs1146593	0.86[ASN][1000 genomes]
rs1146602	0.89[ASN][1000 genomes]
rs1146613	0.83[ASN][1000 genomes]
rs1146616	0.91[ASN][1000 genomes]
rs1146625	0.86[ASN][1000 genomes]
rs1146645	0.95[ASN][1000 genomes]
rs1146647	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs1146649	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1146651	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1146652	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1146656	0.99[ASN][1000 genomes]
rs11579355	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12021750	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12022011	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs12024086	0.90[ASN][1000 genomes]
rs12024645	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12027620	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12032051	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12033058	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12033059	0.82[ASN][1000 genomes]
rs12044025	0.95[JPT][hapmap]
rs12044211	0.81[JPT][hapmap]
rs12045299	0.86[JPT][hapmap]
rs12045363	0.82[ASN][1000 genomes]
rs12076093	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.99[ASN][1000 genomes]
rs12078151	0.99[ASN][1000 genomes]
rs12081710	0.99[ASN][1000 genomes]
rs12090712	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12385715	0.99[ASN][1000 genomes]
rs12401729	0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.91[ASN][1000 genomes]
rs12403889	0.91[ASN][1000 genomes]
rs12405178	0.99[ASN][1000 genomes]
rs12407107	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12409592	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12410373	0.81[JPT][hapmap]
rs1250875	0.81[ASN][1000 genomes]
rs1250876	0.86[JPT][hapmap]
rs1250877	0.81[ASN][1000 genomes]
rs1250878	0.81[ASN][1000 genomes]
rs1250880	0.81[JPT][hapmap]
rs1250881	0.94[ASN][1000 genomes]
rs1250882	0.95[ASN][1000 genomes]
rs1251065	0.81[ASN][1000 genomes]
rs1251078	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1251079	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1251270	0.95[ASN][1000 genomes]
rs1251272	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1251273	0.95[ASN][1000 genomes]
rs1251274	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1251275	0.99[ASN][1000 genomes]
rs12564772	0.82[ASN][1000 genomes]
rs12703	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12726486	0.89[LWK][hapmap];0.88[MKK][hapmap]
rs12732495	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap]
rs12732722	0.86[JPT][hapmap]
rs12744608	0.81[JPT][hapmap]
rs12745456	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12748900	0.84[ASN][1000 genomes]
rs1303870	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1323734	0.80[ASN][1000 genomes]
rs1498313	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1603734	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1621198	0.80[ASN][1000 genomes]
rs1631498	0.81[ASN][1000 genomes]
rs1689271	0.81[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs1694428	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs17097634	0.82[ASN][1000 genomes]
rs17097681	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs17097695	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs17649675	0.81[JPT][hapmap]
rs1767459	0.83[ASN][1000 genomes]
rs1770513	0.81[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1796812	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs1812589	0.99[ASN][1000 genomes]
rs1908089	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1960528	0.80[ASN][1000 genomes]
rs2012536	0.95[ASN][1000 genomes]
rs2047435	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2131558	0.82[ASN][1000 genomes]
rs2307077	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs34045364	0.98[ASN][1000 genomes]
rs34177389	0.98[ASN][1000 genomes]
rs34486572	0.82[ASN][1000 genomes]
rs35290302	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs35591768	0.98[ASN][1000 genomes]
rs36054685	0.95[ASN][1000 genomes]
rs3737574	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs3765682	0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs3795251	0.81[JPT][hapmap]
rs3819949	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4347163	0.87[ASN][1000 genomes]
rs4949884	0.99[ASN][1000 genomes]
rs5019550	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56350137	0.99[ASN][1000 genomes]
rs5745314	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs5745327	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs5745334	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs5745343	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs5745354	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs5745392	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs5745403	1.00[LWK][hapmap];0.80[MKK][hapmap]
rs5745429	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5745448	0.85[JPT][hapmap]
rs5745451	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs5745465	0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs5745523	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs5745532	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs5745537	0.89[LWK][hapmap];0.88[MKK][hapmap]
rs5745542	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs5745546	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs58552356	0.81[ASN][1000 genomes]
rs61676733	0.91[ASN][1000 genomes]
rs6687882	0.81[CHB][hapmap]
rs6695055	0.86[JPT][hapmap]
rs696679	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs699677	0.80[ASN][1000 genomes]
rs699683	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs699824	0.80[ASN][1000 genomes]
rs699825	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7514912	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7516477	0.86[JPT][hapmap]
rs7525919	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7545057	0.81[JPT][hapmap]
rs7548391	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7548991	0.86[JPT][hapmap]
rs814851	0.80[ASN][1000 genomes]
rs814855	0.80[ASN][1000 genomes]
rs815309	0.81[ASN][1000 genomes]
rs931506	0.81[JPT][hapmap]
rs9660848	0.86[JPT][hapmap]

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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1146648	AK5	cis	parietal	SCAN
rs1146648	ACADM	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76257200-76266000	Strong transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:76262400-76266400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:76262400-76267600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:76262400-76267800	Weak transcription	Osteobl	bone
5	chr1:76262400-76269400	Weak transcription	NHDF-Ad	bronchial
6	chr1:76262400-76273200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:76262400-76282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:76262600-76266000	Weak transcription	Liver	Liver
9	chr1:76262600-76266200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:76262600-76288800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:76262600-76294600	Weak transcription	Primary B cells from cord blood	blood
12	chr1:76262800-76266000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:76262800-76266400	Weak transcription	HSMMtube	muscle
14	chr1:76263000-76269400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:76263000-76276600	Weak transcription	Gastric	stomach
16	chr1:76263000-76287400	Weak transcription	Aorta	Aorta
17	chr1:76263000-76289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:76263000-76296200	Weak transcription	Ovary	ovary
19	chr1:76263200-76266800	Weak transcription	GM12878-XiMat	blood
20	chr1:76263200-76268000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:76263200-76277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:76263400-76289000	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:76263600-76284000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:76263800-76266800	Weak transcription	Fetal Brain Female	brain
25	chr1:76264000-76266200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:76264000-76266200	Weak transcription	Lung	lung
27	chr1:76264000-76269400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:76264000-76270600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:76264000-76274200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:76264000-76277000	Weak transcription	HUVEC	blood vessel
31	chr1:76264200-76266000	Weak transcription	NHEK	skin
32	chr1:76264200-76266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:76264200-76266400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:76264200-76266600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:76264200-76268600	Weak transcription	NH-A	brain
36	chr1:76264200-76274800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:76264200-76279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:76264200-76291400	Weak transcription	Psoas Muscle	Psoas
39	chr1:76264400-76266000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:76264400-76266000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:76264400-76266200	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:76264400-76266400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:76264400-76266600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:76264600-76266200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:76264600-76266200	Weak transcription	Fetal Stomach	stomach
46	chr1:76264600-76266200	Weak transcription	Spleen	Spleen
47	chr1:76264600-76266600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:76264600-76267600	Weak transcription	Right Ventricle	heart
49	chr1:76264600-76273600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:76264600-76278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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