Variant report

Variant	rs7610892
Chromosome Location	chr3:24031213-24031214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24025902..24028777-chr3:24030624..24032378,2	K562	blood:
2	chr3:24030711..24032570-chr3:24036287..24038939,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10865791	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs10865792	0.86[ASN][1000 genomes]
rs11129129	0.86[ASN][1000 genomes]
rs11129130	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs11921201	0.86[ASN][1000 genomes]
rs11926688	0.84[ASN][1000 genomes]
rs1533140	0.89[ASW][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1567582	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2003217	0.86[ASN][1000 genomes]
rs36083758	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4078154	0.86[ASN][1000 genomes]
rs4078155	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4241516	0.86[ASN][1000 genomes]
rs4241517	0.81[JPT][hapmap]
rs4241519	0.84[ASN][1000 genomes]
rs4241522	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4292186	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4292187	0.86[ASN][1000 genomes]
rs4293661	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4321479	0.81[JPT][hapmap]
rs4355230	0.84[ASN][1000 genomes]
rs4459841	0.86[ASN][1000 genomes]
rs4564908	0.86[ASN][1000 genomes]
rs4578971	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs4858098	0.81[JPT][hapmap]
rs4858552	0.81[TSI][hapmap]
rs4858558	0.86[ASN][1000 genomes]
rs4858560	0.86[ASN][1000 genomes]
rs4858561	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs4858563	0.86[ASN][1000 genomes]
rs4858567	0.81[JPT][hapmap]
rs4858569	0.81[JPT][hapmap]
rs5023610	0.81[JPT][hapmap]
rs6550810	0.86[ASN][1000 genomes]
rs6550811	0.86[ASN][1000 genomes]
rs6550813	0.85[ASN][1000 genomes]
rs6550816	0.84[ASN][1000 genomes]
rs6550817	0.87[ASN][1000 genomes]
rs6550818	0.81[ASN][1000 genomes]
rs6550820	0.85[ASN][1000 genomes]
rs6550825	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6550826	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6550828	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs6763220	0.85[ASN][1000 genomes]
rs6763241	0.84[ASN][1000 genomes]
rs6779476	0.91[CHB][hapmap]
rs6788335	0.84[ASN][1000 genomes]
rs6789474	0.86[ASN][1000 genomes]
rs6794922	0.81[JPT][hapmap]
rs6800790	0.83[ASW][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6803400	0.84[ASN][1000 genomes]
rs6805489	0.86[ASN][1000 genomes]
rs7610533	0.86[ASN][1000 genomes]
rs7610625	0.86[ASN][1000 genomes]
rs7610993	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616154	0.85[ASN][1000 genomes]
rs7622945	0.86[ASN][1000 genomes]
rs7625196	0.85[ASN][1000 genomes]
rs7626246	0.86[ASN][1000 genomes]
rs7631238	0.86[ASN][1000 genomes]
rs7632867	0.86[ASN][1000 genomes]
rs7635616	0.86[ASN][1000 genomes]
rs7636810	0.81[JPT][hapmap]
rs7643700	0.84[ASN][1000 genomes]
rs7646930	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs7647644	0.81[ASN][1000 genomes]
rs7650339	0.85[ASN][1000 genomes]
rs9831760	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9843244	0.86[ASN][1000 genomes]
rs9848365	0.86[ASN][1000 genomes]
rs9848647	0.86[ASN][1000 genomes]
rs9869684	0.86[ASN][1000 genomes]
rs9883101	0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7610892	TOP2B	cis	cerebellum	SCAN
rs7610892	NEK10	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:24005600-24032800	Weak transcription	NH-A	brain
3	chr3:24018200-24033200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:24018400-24032200	Weak transcription	Fetal Brain Female	brain
5	chr3:24018400-24032400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:24019400-24032800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:24019400-24032800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:24019400-24032800	Weak transcription	Primary T cells from cord blood	blood
9	chr3:24019400-24032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:24019400-24033200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:24019400-24035400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:24019600-24040800	Weak transcription	NHLF	lung
13	chr3:24020200-24032800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:24021400-24032600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:24021400-24032800	Weak transcription	Fetal Heart	heart
16	chr3:24021600-24033200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:24021800-24033200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:24021800-24033400	Weak transcription	NHDF-Ad	bronchial
19	chr3:24023200-24035000	Weak transcription	Right Atrium	heart
20	chr3:24023200-24035200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:24023400-24032200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:24023400-24033200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:24023600-24033400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:24024000-24033200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:24024000-24035200	Weak transcription	Left Ventricle	heart
26	chr3:24024200-24032200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:24024400-24032200	Weak transcription	Brain Substantia Nigra	brain
28	chr3:24025400-24033000	Weak transcription	Primary B cells from cord blood	blood
29	chr3:24029000-24032000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:24029000-24032200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:24029000-24035000	Weak transcription	Lung	lung
32	chr3:24029200-24032000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:24029200-24032600	Weak transcription	HUVEC	blood vessel
34	chr3:24029800-24033200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:24030600-24032000	Weak transcription	Fetal Brain Male	brain
36	chr3:24030800-24040400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:24031200-24031400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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