Variant report

Variant	rs10512491
Chromosome Location	chr17:60045295-60045296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60044075..60048117-chr17:60057244..60060340,4	MCF-7	breast:
2	chr17:60044150..60045918-chr17:60046685..60050147,3	MCF-7	breast:
3	chr17:60003001..60005211-chr17:60042921..60045466,2	MCF-7	breast:
4	chr17:60045013..60047691-chr17:60050667..60053467,2	MCF-7	breast:
5	chr17:60023206..60027330-chr17:60041588..60045632,3	MCF-7	breast:
6	chr17:60003810..60006628-chr17:60043807..60046817,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10221202	0.98[ASN][1000 genomes]
rs1045196	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12601229	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12601523	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12603627	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12603878	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs12937188	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16945638	1.00[MKK][hapmap]
rs16945670	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap]
rs16945724	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16945762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16945785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16945823	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes]
rs1809077	0.82[EUR][1000 genomes]
rs2378946	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28500646	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4280312	0.80[ASN][1000 genomes]
rs72843732	0.82[EUR][1000 genomes]
rs72843737	0.82[EUR][1000 genomes]
rs72843738	0.82[EUR][1000 genomes]
rs72843746	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72843758	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72843759	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72843762	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72843767	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72843769	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72843770	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs72843771	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs72843772	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72843775	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843778	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843782	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72843785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72843788	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72843791	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72843793	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72843797	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72843801	0.89[AMR][1000 genomes]
rs72845403	0.89[AMR][1000 genomes]
rs72845404	0.89[AMR][1000 genomes]
rs72845405	0.89[AMR][1000 genomes]
rs72845406	0.84[AMR][1000 genomes]
rs72845408	0.84[AMR][1000 genomes]
rs753765	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8081200	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs9910451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.94[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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60017800-60050400	Strong transcription	Adipose Nuclei	Adipose
2	chr17:60018000-60046800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:60018000-60072800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr17:60018000-60073400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:60018600-60047000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:60018600-60047200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:60018600-60072600	Strong transcription	Fetal Thymus	thymus
8	chr17:60018800-60073600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:60019200-60051600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:60019600-60050600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:60020200-60050400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr17:60020400-60050600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:60020400-60073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:60020600-60047200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:60020600-60073000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:60020800-60051800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:60020800-60073800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:60021000-60047600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr17:60021000-60050200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr17:60021200-60097000	Strong transcription	Dnd41	blood
21	chr17:60021800-60052400	Strong transcription	HepG2	liver
22	chr17:60021800-60073600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:60022000-60051800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr17:60022200-60052200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr17:60022200-60053200	Strong transcription	Fetal Intestine Large	intestine
26	chr17:60023200-60049400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr17:60023600-60050600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr17:60025400-60074200	Strong transcription	Liver	Liver
29	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:60028400-60059600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:60032800-60058600	Weak transcription	Fetal Heart	heart
32	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
33	chr17:60033200-60056600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:60034800-60052200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:60034800-60072800	Strong transcription	Placenta	Placenta
36	chr17:60035400-60049000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:60035600-60049800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:60035600-60050000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:60035600-60050200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:60035600-60050200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr17:60035800-60046200	Strong transcription	HSMM	muscle
42	chr17:60035800-60046400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr17:60035800-60050200	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr17:60035800-60064400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr17:60036000-60047000	Strong transcription	HUVEC	blood vessel
46	chr17:60036000-60050200	Strong transcription	GM12878-XiMat	blood
47	chr17:60036000-60050400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:60036000-60074000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:60036200-60046600	Strong transcription	HMEC	breast
50	chr17:60036200-60050600	Strong transcription	Osteobl	bone

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