Variant report

Variant	rs7516477
Chromosome Location	chr1:76204502-76204503
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76204248..76206118-chr1:76227096..76229498,2	K562	blood:
2	chr1:76204201..76206191-chr1:76251025..76253822,3	K562	blood:
3	chr1:76189536..76192375-chr1:76202654..76205815,3	K562	blood:
4	chr1:76203557..76205358-chr1:76211524..76214025,2	K562	blood:
5	chr1:76195178..76198710-chr1:76202418..76206872,5	K562	blood:
6	chr1:76204080..76208296-chr1:76250097..76254787,8	K562	blood:
7	chr1:76197210..76199474-chr1:76201595..76205002,3	K562	blood:

Variant related genes	Relation type
ENSG00000178193	Chromatin interaction
ENSG00000207241	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 158 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs1001160	0.84[CEU][hapmap]
rs1021462	0.86[CHB][hapmap]
rs10873738	0.90[JPT][hapmap]
rs10873797	0.84[CEU][hapmap]
rs1093006	0.83[ASN][1000 genomes]
rs1093009	0.83[ASN][1000 genomes]
rs11161439	0.84[ASN][1000 genomes]
rs11161447	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11161465	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11161600	0.80[ASN][1000 genomes]
rs11161602	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11161731	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11161848	0.84[CEU][hapmap]
rs11161852	0.82[CHB][hapmap]
rs11161887	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs11164035	0.84[ASN][1000 genomes]
rs11164037	0.84[ASN][1000 genomes]
rs1144328	0.81[JPT][hapmap]
rs1144331	0.81[JPT][hapmap]
rs1144333	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1144337	0.81[JPT][hapmap]
rs1144342	0.81[JPT][hapmap]
rs1146572	0.89[ASN][1000 genomes]
rs1146577	0.83[ASN][1000 genomes]
rs1146587	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146592	0.85[ASN][1000 genomes]
rs1146593	0.83[ASN][1000 genomes]
rs1146647	0.81[JPT][hapmap]
rs1146648	0.86[JPT][hapmap]
rs1146649	0.81[JPT][hapmap]
rs1146651	0.85[JPT][hapmap]
rs1146652	0.81[JPT][hapmap]
rs11578480	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs11588643	0.84[CEU][hapmap]
rs1159215	0.84[CEU][hapmap]
rs12021750	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12022011	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12024645	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12027620	0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs12032051	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12033058	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12044025	0.90[JPT][hapmap]
rs12045299	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12076093	0.86[JPT][hapmap]
rs12090712	0.85[JPT][hapmap]
rs12130832	0.91[CEU][hapmap]
rs12131344	0.96[CEU][hapmap]
rs12132750	0.95[CEU][hapmap]
rs12142247	0.91[CEU][hapmap]
rs12401729	0.81[CHB][hapmap]
rs12407107	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12409592	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1250875	0.89[ASN][1000 genomes]
rs1250876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1250877	0.89[ASN][1000 genomes]
rs1250878	0.89[ASN][1000 genomes]
rs1250880	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251065	0.89[ASN][1000 genomes]
rs1251078	0.91[JPT][hapmap]
rs1251079	0.91[JPT][hapmap]
rs1251272	0.84[JPT][hapmap]
rs1251274	0.81[JPT][hapmap]
rs12563737	0.90[ASN][1000 genomes]
rs12703	0.81[JPT][hapmap]
rs12728962	0.80[ASN][1000 genomes]
rs12732722	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12744608	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12745456	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12747967	0.84[ASN][1000 genomes]
rs12756349	0.80[ASN][1000 genomes]
rs1303870	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs1323734	0.83[ASN][1000 genomes]
rs1391518	0.84[ASN][1000 genomes]
rs1391520	0.84[ASN][1000 genomes]
rs1498311	0.84[CEU][hapmap]
rs1498313	0.86[JPT][hapmap]
rs1603734	0.86[JPT][hapmap]
rs1621198	0.83[ASN][1000 genomes]
rs1628063	0.84[CEU][hapmap]
rs1630587	0.84[CEU][hapmap]
rs1631498	0.83[ASN][1000 genomes]
rs1689270	0.84[CEU][hapmap]
rs1694421	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1694428	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs17097681	0.81[CHB][hapmap]
rs17647178	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs1767457	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1767459	0.85[ASN][1000 genomes]
rs1770513	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1770889	0.84[CEU][hapmap]
rs1796813	0.84[CEU][hapmap]
rs1796815	0.87[CEU][hapmap]
rs1796827	0.84[CEU][hapmap]
rs1826978	0.85[ASN][1000 genomes]
rs1846233	0.96[CEU][hapmap]
rs1856791	0.83[CEU][hapmap]
rs1908089	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1960528	0.83[ASN][1000 genomes]
rs2029682	0.84[CEU][hapmap]
rs2307077	0.81[JPT][hapmap]
rs35290302	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs35837767	0.84[ASN][1000 genomes]
rs3737574	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3765682	0.81[CHB][hapmap]
rs3819949	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4638068	0.96[CEU][hapmap]
rs5745314	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs5745327	0.81[JPT][hapmap]
rs5745331	0.84[CEU][hapmap]
rs5745334	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs5745343	0.81[JPT][hapmap]
rs5745347	0.84[CEU][hapmap]
rs5745383	0.83[CEU][hapmap]
rs5745392	0.81[JPT][hapmap]
rs5745394	0.83[CEU][hapmap]
rs5745429	0.82[CHB][hapmap]
rs5745430	0.84[CEU][hapmap]
rs5745448	0.80[JPT][hapmap]
rs5745451	0.81[JPT][hapmap]
rs5745465	0.81[CHB][hapmap]
rs5745523	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs5745532	0.85[CHB][hapmap]
rs5745542	0.81[CHB][hapmap]
rs5745543	0.83[CEU][hapmap]
rs5745545	0.84[CEU][hapmap]
rs5745546	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5745547	0.84[CEU][hapmap]
rs6656501	0.84[CEU][hapmap]
rs6676182	0.90[ASN][1000 genomes]
rs6687882	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs6695055	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs67108483	0.84[ASN][1000 genomes]
rs696677	0.82[ASN][1000 genomes]
rs696679	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs699677	0.83[ASN][1000 genomes]
rs699683	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs699824	0.83[ASN][1000 genomes]
rs699825	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs71502708	0.83[ASN][1000 genomes]
rs7514912	0.86[JPT][hapmap]
rs7525919	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7548391	0.86[JPT][hapmap]
rs7548695	0.89[ASN][1000 genomes]
rs7548991	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs814851	0.83[ASN][1000 genomes]
rs814855	0.83[ASN][1000 genomes]
rs814897	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs815301	0.83[ASN][1000 genomes]
rs815303	0.81[ASN][1000 genomes]
rs815305	0.82[ASN][1000 genomes]
rs815309	0.86[ASN][1000 genomes]
rs9660848	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv871572	chr1:76161889-76208488	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	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
6	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7516477	SNORD45B	cis	cerebellum	SCAN
rs7516477	RABGGTB	cis	cerebellum	SCAN
rs7516477	SNORD45B	cis	parietal	SCAN
rs7516477	PIGK	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76190800-76207200	Weak transcription	Spleen	Spleen
2	chr1:76190800-76208000	Weak transcription	Gastric	stomach
3	chr1:76191200-76219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:76191800-76208000	Weak transcription	A549	lung
5	chr1:76191800-76208200	Weak transcription	Brain Substantia Nigra	brain
6	chr1:76191800-76209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:76192000-76208000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:76192000-76210200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:76192000-76220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:76192000-76220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:76192000-76227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:76192200-76204600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:76192200-76217800	Weak transcription	Fetal Brain Male	brain
14	chr1:76192200-76222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:76192400-76207600	Weak transcription	Colonic Mucosa	Colon
16	chr1:76193600-76220200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:76193800-76207800	Weak transcription	Right Ventricle	heart
18	chr1:76193800-76208000	Weak transcription	Hela-S3	cervix
19	chr1:76193800-76208600	Weak transcription	Small Intestine	intestine
20	chr1:76193800-76220200	Weak transcription	Fetal Heart	heart
21	chr1:76194000-76208000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:76195600-76219600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:76195800-76213800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:76196000-76210800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:76196000-76222000	Strong transcription	Liver	Liver
26	chr1:76196200-76212600	Strong transcription	Fetal Thymus	thymus
27	chr1:76196400-76210800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:76196400-76213000	Strong transcription	Dnd41	blood
29	chr1:76197600-76209600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:76197600-76211400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:76197600-76212000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:76197600-76219400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:76197800-76207400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:76197800-76210600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:76198000-76210400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:76198200-76209800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:76198200-76210400	Strong transcription	Adipose Nuclei	Adipose
38	chr1:76198200-76210600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:76198400-76210400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:76198600-76205400	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:76198600-76208000	Weak transcription	NHLF	lung
42	chr1:76198600-76210200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:76198600-76210400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:76198600-76211600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:76198600-76212000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:76198800-76209400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:76198800-76210600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:76198800-76210800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:76199000-76207400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:76199000-76210200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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