Variant report

Variant	rs10857561
Chromosome Location	chr10:49608638-49608639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr10:49608052-49608676	K562	blood:	n/a	n/a
2	FOS	chr10:49608142-49608673	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr10:49608540-49608690	HCPEpiC	choroid plexus:	n/a	n/a
4	BATF	chr10:49608340-49608776	GM12878	blood:	n/a	n/a
5	CTCF	chr10:49608500-49608650	HBMEC	blood vessel:	n/a	n/a
6	MAFK	chr10:49608565-49608765	HepG2	liver:	n/a	n/a
7	ARID3A	chr10:49608088-49608879	K562	blood:	n/a	n/a
8	CTCF	chr10:49608500-49608650	BJ	skin:	n/a	n/a
9	RUNX3	chr10:49608347-49608955	GM12878	blood:	n/a	chr10:49608734-49608743 chr10:49608734-49608743
10	CTCF	chr10:49608500-49608650	HCPEpiC	choroid plexus:	n/a	n/a
11	MAFK	chr10:49608395-49608738	IMR90	lung:	n/a	n/a
12	CTCF	chr10:49608520-49608670	HRE	kidney:	n/a	n/a
13	ZNF263	chr10:49607361-49608750	HEK293-T-REx	kidney:	n/a	n/a
14	IKZF1	chr10:49608373-49608700	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:49605353..49609385-chr10:49612341..49615386,5	K562	blood:
2	chr10:49514733..49517675-chr10:49606696..49609603,2	K562	blood:
3	chr10:49514542..49516292-chr10:49606736..49609603,3	K562	blood:

Variant related genes	Relation type
MAPK8	TF binding region
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10508901	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10508903	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10745266	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs10776595	0.95[JPT][hapmap]
rs10776596	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs10776598	0.82[ASN][1000 genomes]
rs10776600	0.80[EUR][1000 genomes]
rs10857560	0.87[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10857563	0.81[ASN][1000 genomes]
rs10857564	0.81[ASN][1000 genomes]
rs10857567	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11101306	0.83[ASN][1000 genomes]
rs11101317	0.87[ASN][1000 genomes]
rs11101318	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11101320	0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11598434	0.82[ASN][1000 genomes]
rs11599396	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12411830	0.89[JPT][hapmap]
rs1345103	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1919708	0.81[ASN][1000 genomes]
rs1919712	0.95[JPT][hapmap]
rs1919713	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.87[ASN][1000 genomes]
rs2017750	0.81[CHD][hapmap]
rs2263102	0.84[ASN][1000 genomes]
rs2289805	0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2377351	0.83[EUR][1000 genomes]
rs2440861	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2463959	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2463960	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2590381	0.84[ASN][1000 genomes]
rs2698761	0.87[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2698766	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2698767	0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2698768	0.81[ASN][1000 genomes]
rs2889611	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2921271	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3827680	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4838590	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4838591	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6537561	0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7072515	0.95[JPT][hapmap]
rs7075976	0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7076214	0.87[ASN][1000 genomes]
rs7086275	0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7101060	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs72794398	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs734371	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7904142	0.86[ASN][1000 genomes]
rs7912697	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7924070	0.85[ASN][1000 genomes]
rs8428	0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs867631	0.81[ASN][1000 genomes]
rs874208	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs883604	0.81[ASN][1000 genomes]
rs9284	0.95[JPT][hapmap]
rs9888128	0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1039508	chr10:49595718-49654403	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3379459	chr10:49608555-49608765	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10857561	MAPK8	cis	normal skin	skin_eQTL
rs10857561	MAPK8	cis	cerebellum	SCAN
rs10857561	MAPK8	Cis_1M	lymphoblastoid	RTeQTL
rs10857561	MAPK8	cis	Thyroid	GTEx
rs10857561	MSMB	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49595000-49616000	Weak transcription	Primary B cells from cord blood	blood
2	chr10:49598600-49619800	Weak transcription	Fetal Intestine Small	intestine
3	chr10:49598800-49612800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:49599200-49622200	Weak transcription	HepG2	liver
5	chr10:49599800-49618000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr10:49600000-49612400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr10:49600000-49613400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr10:49600000-49613600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr10:49600000-49618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr10:49600200-49612400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr10:49600200-49617400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:49600200-49618200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:49600400-49616800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr10:49600400-49620200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:49601200-49613800	Weak transcription	Primary T cells from cord blood	blood
16	chr10:49604200-49609200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:49605200-49618000	Weak transcription	Fetal Muscle Leg	muscle
18	chr10:49606000-49609000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:49606200-49608800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr10:49606200-49609200	Enhancers	Brain Anterior Caudate	brain
21	chr10:49606200-49609200	Enhancers	HSMMtube	muscle
22	chr10:49606200-49609400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr10:49606200-49609400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:49606200-49609800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr10:49606200-49609800	Enhancers	Brain Angular Gyrus	brain
26	chr10:49606400-49609200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:49606400-49609200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr10:49606400-49609200	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr10:49606400-49609200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr10:49606400-49609200	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr10:49606400-49609200	Enhancers	K562	blood
32	chr10:49606600-49609200	Enhancers	H1 Cell Line	embryonic stem cell
33	chr10:49606600-49609400	Enhancers	Fetal Brain Male	brain
34	chr10:49606800-49609000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr10:49606800-49609200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:49606800-49609200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr10:49606800-49609200	Enhancers	Adipose Nuclei	Adipose
38	chr10:49606800-49609800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:49606800-49619800	Weak transcription	Fetal Stomach	stomach
40	chr10:49607000-49608800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr10:49607000-49608800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr10:49607000-49608800	Enhancers	NH-A	brain
43	chr10:49607000-49608800	Enhancers	NHLF	lung
44	chr10:49607000-49609000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr10:49607000-49609200	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr10:49607000-49609200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:49607000-49609200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr10:49607000-49609200	Enhancers	HUVEC	blood vessel
49	chr10:49607000-49609800	Enhancers	HMEC	breast
50	chr10:49607000-49612400	Weak transcription	Dnd41	blood

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