Variant report

Variant	rs4140593
Chromosome Location	chr6:36464958-36464959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36462201..36467038-chr6:36561436..36566135,7	K562	blood:
2	chr6:36464672..36468540-chr6:36473344..36476121,3	K562	blood:
3	chr6:36462622..36466969-chr6:36560002..36564698,6	K562	blood:
4	chr6:36408368..36410814-chr6:36464832..36467781,2	K562	blood:

Variant related genes	Relation type
ENSG00000112078	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000179165	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1003250	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10440841	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10947609	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12209346	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12214285	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12215889	0.87[ASN][1000 genomes]
rs1570368	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1744654	0.86[ASN][1000 genomes]
rs2146333	0.82[MKK][hapmap]
rs2239807	0.86[MKK][hapmap]
rs2300064	0.86[MKK][hapmap]
rs3752478	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3798471	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711450	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711452	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711453	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs515129	0.86[ASN][1000 genomes]
rs515186	0.82[ASN][1000 genomes]
rs517890	0.85[ASN][1000 genomes]
rs522179	0.86[ASN][1000 genomes]
rs544267	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs546272	0.87[ASN][1000 genomes]
rs546353	0.87[ASN][1000 genomes]
rs547026	0.88[ASN][1000 genomes]
rs547966	0.87[ASN][1000 genomes]
rs566742	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs57389119	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584196	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs584418	0.86[ASN][1000 genomes]
rs595954	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597153	0.87[ASN][1000 genomes]
rs600192	0.88[ASN][1000 genomes]
rs605684	0.91[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs609067	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs614028	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs619011	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs621796	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs628213	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs628314	0.87[ASN][1000 genomes]
rs629297	0.87[ASN][1000 genomes]
rs629560	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs629721	0.81[ASN][1000 genomes]
rs632943	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6457918	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648125	0.87[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs659726	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs664370	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs668499	0.81[CHB][hapmap]
rs6905347	0.82[MKK][hapmap]
rs6923993	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6926522	0.82[MKK][hapmap]
rs6927896	0.86[MKK][hapmap]
rs6941918	0.86[ASN][1000 genomes]
rs73411054	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7744363	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853873	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs853881	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853882	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs860513	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9296184	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9357214	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470274	0.80[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9470278	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs9470285	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9470309	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4140593	PXT1	cis	lymphoblastoid	seeQTL
rs4140593	CPNE5	cis	cerebellum	SCAN
rs4140593	C6orf1	cis	parietal	SCAN
rs4140593	TULP1	cis	cerebellum	SCAN
rs4140593	ETV7	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36411600-36476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:36430800-36488800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:36437800-36468000	Strong transcription	Fetal Muscle Leg	muscle
4	chr6:36437800-36477600	Strong transcription	Fetal Thymus	thymus
5	chr6:36447200-36477600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:36447400-36477800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:36450000-36479800	Weak transcription	Stomach Mucosa	stomach
8	chr6:36455200-36476400	Weak transcription	Pancreas	Pancrea
9	chr6:36456000-36467600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:36456400-36512600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:36457200-36469600	Strong transcription	Fetal Intestine Small	intestine
12	chr6:36457400-36484400	Weak transcription	Right Atrium	heart
13	chr6:36459400-36468000	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr6:36459600-36469600	Strong transcription	Fetal Stomach	stomach
15	chr6:36459800-36467000	Weak transcription	Gastric	stomach
16	chr6:36460600-36467800	Strong transcription	HSMMtube	muscle
17	chr6:36460600-36468000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:36461000-36466000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:36461000-36469800	Strong transcription	Fetal Intestine Large	intestine
20	chr6:36461200-36465200	Strong transcription	Brain Germinal Matrix	brain
21	chr6:36461200-36465400	Strong transcription	A549	lung
22	chr6:36461200-36465600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:36461200-36465600	Strong transcription	Rectal Smooth Muscle	rectum
24	chr6:36461200-36465600	Strong transcription	Thymus	Thymus
25	chr6:36461200-36466000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:36461200-36468000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:36461200-36468000	Strong transcription	Liver	Liver
28	chr6:36461200-36468000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr6:36461200-36468000	Strong transcription	Fetal Brain Female	brain
30	chr6:36461200-36468000	Strong transcription	Fetal Lung	lung
31	chr6:36461200-36468000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr6:36461200-36468000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr6:36461200-36468000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:36461200-36468000	Strong transcription	NH-A	brain
35	chr6:36461200-36468800	Strong transcription	Placenta	Placenta
36	chr6:36461200-36468800	Strong transcription	Dnd41	blood
37	chr6:36461200-36469200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr6:36461200-36472200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:36461200-36475400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:36461200-36475400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr6:36461400-36465600	Strong transcription	K562	blood
42	chr6:36461400-36468000	Strong transcription	HSMM	muscle
43	chr6:36461400-36481400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:36461600-36476400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:36461800-36465800	Strong transcription	NHDF-Ad	bronchial
46	chr6:36461800-36468400	Strong transcription	Left Ventricle	heart
47	chr6:36462000-36465200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:36462000-36465400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:36462000-36465400	Strong transcription	NHEK	skin
50	chr6:36462000-36466000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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