Variant report

Variant	rs10517225
Chromosome Location	chr4:48545814-48545815
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48544834..48546523-chr4:48551748..48553430,2	K562	blood:
2	chr4:48537925..48542072-chr4:48545238..48547735,4	MCF-7	breast:
3	chr4:48540734..48543756-chr4:48544156..48546827,3	K562	blood:
4	chr4:48544798..48547202-chr4:48547585..48550230,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11727472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932126	0.86[EUR][1000 genomes]
rs12498166	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505376	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12506770	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508327	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13110719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565218	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1565221	0.86[EUR][1000 genomes]
rs16861344	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1702800	1.00[ASN][1000 genomes]
rs1712762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17609521	0.86[EUR][1000 genomes]
rs17609535	0.86[EUR][1000 genomes]
rs17609556	0.86[EUR][1000 genomes]
rs17609614	0.86[EUR][1000 genomes]
rs17609740	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609761	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17655725	0.86[EUR][1000 genomes]
rs17655741	0.86[EUR][1000 genomes]
rs17656189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656212	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656255	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814784	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1850520	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581223	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945331	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3107023	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695378	0.81[EUR][1000 genomes]
rs4695388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695389	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55730515	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55884608	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55986500	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56932035	0.86[EUR][1000 genomes]
rs57676508	0.86[EUR][1000 genomes]
rs57893769	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58038882	0.86[EUR][1000 genomes]
rs58244627	0.86[EUR][1000 genomes]
rs58707818	0.86[EUR][1000 genomes]
rs60891069	0.86[EUR][1000 genomes]
rs6447646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447648	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810911	0.86[EUR][1000 genomes]
rs6825104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847014	0.86[EUR][1000 genomes]
rs6852840	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs707719	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814762	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73814763	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73814781	1.00[AFR][1000 genomes]
rs73814782	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814798	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817807	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817808	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817809	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817826	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817827	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693468	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7695730	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776596	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs776598	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776599	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938790	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48498600-48593000	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr4:48499000-48578800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:48499000-48589400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr4:48499600-48581400	Strong transcription	Dnd41	blood
5	chr4:48500200-48588800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:48501400-48578600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:48504400-48575400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:48505200-48575400	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:48507200-48564000	Strong transcription	Fetal Thymus	thymus
10	chr4:48507600-48568600	Strong transcription	Primary T cells from cord blood	blood
11	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
12	chr4:48519400-48566200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:48522600-48563200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:48525000-48595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:48525200-48552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:48533000-48552600	Weak transcription	Aorta	Aorta
18	chr4:48533600-48547000	Weak transcription	Fetal Brain Male	brain
19	chr4:48535000-48548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:48538600-48547200	Weak transcription	NHLF	lung
21	chr4:48540600-48580400	Strong transcription	Fetal Intestine Large	intestine
22	chr4:48540800-48550200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:48540800-48576000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:48541000-48580600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:48541000-48587800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:48541200-48548200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:48541200-48548400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:48541200-48548600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:48541200-48548600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr4:48541200-48553600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:48541200-48560000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:48541200-48566600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr4:48541200-48567000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:48541200-48594000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:48541400-48546000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:48541400-48548200	Strong transcription	Rectal Smooth Muscle	rectum
37	chr4:48541400-48548400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:48541400-48548400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:48541400-48548600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:48541400-48548600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:48541400-48548600	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:48541400-48548600	Strong transcription	Fetal Lung	lung
43	chr4:48541400-48554400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:48541400-48554400	Strong transcription	Brain Hippocampus Middle	brain
45	chr4:48541400-48555800	Strong transcription	Primary B cells from cord blood	blood
46	chr4:48541400-48566200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:48541400-48581200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr4:48541600-48548400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:48541600-48548400	Strong transcription	NHEK	skin
50	chr4:48541600-48548600	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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