Variant report

Variant	rs10942597
Chromosome Location	chr5:89807395-89807396
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	chr5:89703969..89706957-chr5:89807176..89809846,2	K562	blood:
2	chr5:89797561..89800163-chr5:89806524..89808529,2	K562	blood:

Variant related genes	Relation type
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10043836	0.85[JPT][hapmap]
rs10058765	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10060427	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10062714	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10062924	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10068473	0.85[JPT][hapmap]
rs10072105	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs1028191	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1028192	0.85[JPT][hapmap]
rs1033290	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10462342	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs10473936	0.88[EUR][1000 genomes]
rs1047787	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10514327	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10514333	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10942596	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10942605	0.85[JPT][hapmap]
rs10942606	0.85[JPT][hapmap]
rs1160121	0.85[JPT][hapmap]
rs11743030	0.81[CHB][hapmap]
rs12188928	0.85[JPT][hapmap]
rs12516985	0.83[JPT][hapmap]
rs12655180	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13182165	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13185955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1673378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1673379	0.92[JPT][hapmap]
rs16868957	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1700510	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs1700511	0.92[JPT][hapmap]
rs1812737	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1878878	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1993474	0.84[JPT][hapmap]
rs2176624	0.85[JPT][hapmap]
rs2222242	0.85[JPT][hapmap]
rs2366771	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2366773	0.92[JPT][hapmap]
rs2366774	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2366777	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3087840	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35407205	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3805483	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs474800	0.81[EUR][1000 genomes]
rs490812	0.92[JPT][hapmap]
rs4916681	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4916684	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4916686	0.85[JPT][hapmap]
rs4916813	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs498491	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs499148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501640	0.91[EUR][1000 genomes]
rs502596	0.92[JPT][hapmap]
rs552314	0.81[EUR][1000 genomes]
rs558809	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs587818	0.91[EUR][1000 genomes]
rs603015	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs603870	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs616379	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617379	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs618355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs623761	0.81[EUR][1000 genomes]
rs637442	0.92[JPT][hapmap]
rs645652	0.81[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs648430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs666659	0.86[EUR][1000 genomes]
rs67376567	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6863710	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6878917	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6883872	0.92[JPT][hapmap]
rs6888355	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs688956	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs688960	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6897910	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6898209	0.85[JPT][hapmap]
rs7716979	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7717423	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7721198	0.82[JPT][hapmap]
rs7726624	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs7729703	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7732169	0.85[JPT][hapmap]
rs9293550	0.85[JPT][hapmap]
rs963866	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs977906	0.85[JPT][hapmap]
rs9790907	0.81[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10942597	LYSMD3	cis	normal skin	skin_eQTL
rs10942597	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL
rs10942597	GPR98	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:89773800-89816000	Weak transcription	HepG2	liver
3	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:89774000-89814600	Weak transcription	Dnd41	blood
5	chr5:89774400-89814600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:89780400-89810800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:89783800-89813400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:89784800-89814600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:89785400-89814600	Weak transcription	NHLF	lung
11	chr5:89790200-89809600	Weak transcription	GM12878-XiMat	blood
12	chr5:89791400-89814600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:89791600-89813800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:89791600-89814600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:89792200-89810400	Weak transcription	Left Ventricle	heart
16	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
17	chr5:89797600-89814600	Weak transcription	Adipose Nuclei	Adipose
18	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
19	chr5:89798000-89814600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:89799600-89817200	Weak transcription	NHDF-Ad	bronchial
21	chr5:89799800-89814600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:89800000-89807600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:89800000-89814400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr5:89800000-89814600	Weak transcription	NHEK	skin
25	chr5:89800800-89808200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:89800800-89808600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:89800800-89811600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:89800800-89814600	Weak transcription	HMEC	breast
29	chr5:89801000-89813600	Weak transcription	NH-A	brain
30	chr5:89801000-89814600	Weak transcription	HUVEC	blood vessel
31	chr5:89801200-89809200	Weak transcription	A549	lung
32	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:89803200-89810400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:89803200-89817600	Weak transcription	Small Intestine	intestine
35	chr5:89804000-89813400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:89804000-89816400	Weak transcription	Thymus	Thymus
37	chr5:89804800-89814600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:89805600-89812200	Weak transcription	HSMM	muscle
39	chr5:89805600-89819800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr5:89805600-89823200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:89805800-89819800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:89806000-89814800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:89806200-89807400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:89806400-89809800	Weak transcription	K562	blood
45	chr5:89806400-89818200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr5:89806600-89807400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:89806600-89808600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:89807000-89810400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:89807200-89807600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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