Variant report

Variant	rs923757
Chromosome Location	chr10:25357584-25357585
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:25352997..25355657-chr10:25355970..25357954,2	K562	blood:
2	chr10:25356543..25358700-chr10:25359934..25363281,3	K562	blood:
3	chr10:25350138..25352241-chr10:25355108..25357944,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10764518	1.00[YRI][hapmap]
rs10828750	0.91[ASN][1000 genomes]
rs10828751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10828752	0.98[ASN][1000 genomes]
rs10828754	0.91[ASN][1000 genomes]
rs10828755	0.94[ASN][1000 genomes]
rs11014365	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs11014366	1.00[YRI][hapmap]
rs11014367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11014368	0.90[ASN][1000 genomes]
rs11014375	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11014379	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11014389	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs12219239	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12241661	0.84[ASN][1000 genomes]
rs12764623	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12773782	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1492606	0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1492607	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1552770	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1552771	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1907790	0.89[ASN][1000 genomes]
rs1963584	0.83[ASN][1000 genomes]
rs2087781	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2131275	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2131276	1.00[YRI][hapmap]
rs2367507	0.83[ASN][1000 genomes]
rs4237369	0.84[ASN][1000 genomes]
rs4508094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4749000	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4749004	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4749005	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6482468	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7896122	0.84[ASN][1000 genomes]
rs7911863	0.84[ASN][1000 genomes]
rs7913853	1.00[YRI][hapmap]
rs902906	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[ASN][1000 genomes]
rs923758	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv550224	chr10:25335854-25385858	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1036683	chr10:25337592-25398119	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv894969	chr10:25345720-25395579	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs923757	THNSL1	cis	cerebellum	SCAN
rs923757	PIP4K2A	cis	parietal	SCAN
rs923757	THNSL1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25356400-25358200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr10:25356600-25358200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:25356600-25358200	Enhancers	HMEC	breast
4	chr10:25356600-25358200	Enhancers	NHEK	skin
5	chr10:25356800-25357600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr10:25356800-25357600	Enhancers	Brain Cingulate Gyrus	brain
7	chr10:25356800-25357800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr10:25356800-25357800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:25356800-25357800	Enhancers	HepG2	liver
10	chr10:25356800-25357800	Enhancers	NH-A	brain
11	chr10:25356800-25357800	Enhancers	Osteobl	bone
12	chr10:25356800-25358000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr10:25356800-25358000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:25356800-25358000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:25356800-25358000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:25356800-25358000	Enhancers	HUVEC	blood vessel
17	chr10:25356800-25358200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr10:25356800-25358800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:25357000-25357600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:25357000-25357600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr10:25357000-25357600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
22	chr10:25357000-25357600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:25357000-25357600	Enhancers	NHDF-Ad	bronchial
24	chr10:25357000-25357800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr10:25357000-25357800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
26	chr10:25357000-25357800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr10:25357000-25357800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:25357000-25357800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:25357200-25357600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr10:25357200-25357600	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr10:25357200-25357800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr10:25357400-25357600	Enhancers	Brain Angular Gyrus	brain
33	chr10:25357400-25357800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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