Variant report

Variant	rs4636555
Chromosome Location	chr10:18903605-18903606
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:18892806..18896035-chr10:18901171..18903670,3	K562	blood:
2	chr10:18897158..18899309-chr10:18901969..18904753,2	K562	blood:
3	chr10:18902407..18904405-chr10:18907032..18908667,2	K562	blood:
4	chr10:18896603..18898658-chr10:18901969..18903863,2	K562	blood:
5	chr10:18901454..18904568-chr10:18946720..18950711,3	K562	blood:

Variant related genes	Relation type
ENSG00000152487	Chromatin interaction
ENSG00000165997	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10732437	1.00[ASN][1000 genomes]
rs10741086	1.00[CHB][hapmap]
rs10764566	0.84[TSI][hapmap]
rs10764587	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10764661	1.00[ASN][1000 genomes]
rs10828835	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs10828859	0.81[CEU][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap]
rs10828970	0.96[EUR][1000 genomes]
rs10829156	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10829157	1.00[ASN][1000 genomes]
rs10829199	1.00[ASN][1000 genomes]
rs11015307	0.80[CEU][hapmap]
rs12359508	0.91[EUR][1000 genomes]
rs12570585	0.89[EUR][1000 genomes]
rs12772534	0.96[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs12781038	0.91[EUR][1000 genomes]
rs1880682	0.83[MKK][hapmap];0.82[TSI][hapmap]
rs1917209	1.00[ASN][1000 genomes]
rs1917823	1.00[ASN][1000 genomes]
rs4338439	1.00[ASN][1000 genomes]
rs4456162	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4475829	0.93[EUR][1000 genomes]
rs4475830	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484992	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4578284	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4606373	1.00[ASN][1000 genomes]
rs4634984	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748474	1.00[CHD][hapmap]
rs4748476	1.00[CHB][hapmap]
rs4748479	1.00[ASN][1000 genomes]
rs4748480	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4748489	0.91[EUR][1000 genomes]
rs4748491	0.89[EUR][1000 genomes]
rs4748493	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4748494	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4748495	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4748504	1.00[ASN][1000 genomes]
rs4748507	1.00[ASN][1000 genomes]
rs62636215	0.89[ASN][1000 genomes]
rs6482529	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs6482534	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482545	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6482546	0.89[ASN][1000 genomes]
rs6482567	1.00[ASN][1000 genomes]
rs7068575	0.91[EUR][1000 genomes]
rs7071192	0.87[EUR][1000 genomes]
rs7073651	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7075151	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7075304	0.88[EUR][1000 genomes]
rs7075678	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7077786	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7080903	0.87[EUR][1000 genomes]
rs7081435	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7081811	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs7082094	0.91[EUR][1000 genomes]
rs7082235	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7088214	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7090926	0.89[ASN][1000 genomes]
rs7091578	0.91[EUR][1000 genomes]
rs7092437	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs7093907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7095666	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7098313	0.83[MKK][hapmap];0.84[TSI][hapmap]
rs7098721	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099307	1.00[CHB][hapmap];0.82[MKK][hapmap];1.00[ASN][1000 genomes]
rs7099975	0.83[EUR][1000 genomes]
rs7100884	1.00[ASN][1000 genomes]
rs7101269	0.84[EUR][1000 genomes]
rs7895709	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895775	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907153	0.80[MKK][hapmap]
rs7908550	1.00[ASN][1000 genomes]
rs7909552	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7911922	1.00[ASN][1000 genomes]
rs7918933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7923072	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8181345	1.00[ASN][1000 genomes]
rs9731044	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34545	chr10:18821185-18908294	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv2757371	chr10:18835325-18906507	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2759736	chr10:18835325-18906507	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv466760	chr10:18839350-18905935	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv550044	chr10:18839350-18905935	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4636555	NSUN6	cis	Nerve Tibial	GTEx
rs4636555	OLAH	cis	parietal	SCAN
rs4636555	NSUN6	cis	parietal	SCAN
rs4636555	NSUN6	cis	cerebellum	SCAN
rs4636555	PTPLA	cis	cerebellum	SCAN
rs4636555	TRDMT1	cis	parietal	SCAN
rs4636555	RP11-499P20.2	cis	lung	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18848400-18915800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr10:18849800-18910800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr10:18863000-18910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:18867800-18916400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr10:18868000-18916200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr10:18868200-18904800	Weak transcription	HSMMtube	muscle
7	chr10:18869800-18910800	Weak transcription	Right Ventricle	heart
8	chr10:18870600-18908400	Weak transcription	Brain Substantia Nigra	brain
9	chr10:18870600-18916000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:18871600-18910000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr10:18872800-18916000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:18873200-18908200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr10:18873600-18916000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:18875000-18916000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:18875600-18912600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:18877200-18916200	Weak transcription	Thymus	Thymus
17	chr10:18877200-18916400	Weak transcription	Spleen	Spleen
18	chr10:18877400-18916200	Weak transcription	Pancreas	Pancrea
19	chr10:18877400-18916400	Weak transcription	Psoas Muscle	Psoas
20	chr10:18877600-18916400	Weak transcription	Gastric	stomach
21	chr10:18878000-18915600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr10:18881400-18916400	Weak transcription	Brain Angular Gyrus	brain
23	chr10:18882000-18916200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr10:18884200-18916400	Weak transcription	Aorta	Aorta
25	chr10:18884600-18916400	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:18884800-18909400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr10:18885200-18904400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr10:18885400-18916200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr10:18885400-18916400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr10:18891600-18916400	Weak transcription	Lung	lung
31	chr10:18895400-18908000	Weak transcription	Fetal Brain Male	brain
32	chr10:18895600-18916400	Weak transcription	Left Ventricle	heart
33	chr10:18896400-18907200	Strong transcription	Primary T cells from cord blood	blood
34	chr10:18896600-18916400	Weak transcription	Colon Smooth Muscle	Colon
35	chr10:18896600-18916400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr10:18896800-18916000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr10:18897200-18906600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr10:18897200-18916400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr10:18898400-18916400	Weak transcription	Fetal Kidney	kidney
40	chr10:18898400-18916400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr10:18900000-18904600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:18900000-18906600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr10:18900000-18910000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr10:18900000-18912600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:18900000-18915800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr10:18900000-18915800	Weak transcription	NHEK	skin
47	chr10:18900000-18916200	Weak transcription	NHLF	lung
48	chr10:18900000-18916600	Weak transcription	Stomach Mucosa	stomach
49	chr10:18900200-18906400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr10:18900200-18907400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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