Variant report

Variant	rs4711453
Chromosome Location	chr6:36439391-36439392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36431159..36433332-chr6:36438906..36441018,2	K562	blood:
2	chr6:36437874..36441513-chr6:36442107..36445031,4	K562	blood:
3	chr6:36408380..36411349-chr6:36438111..36440624,2	K562	blood:
4	chr6:36438735..36444025-chr6:36445712..36451079,5	K562	blood:
5	chr6:36437672..36440235-chr6:36445190..36447212,2	K562	blood:
6	chr6:36438533..36440442-chr6:36481123..36483555,2	K562	blood:

Variant related genes	Relation type
ENSG00000112078	Chromatin interaction
ENSG00000179165	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1003250	1.00[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];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10440841	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1061632	0.80[MKK][hapmap]
rs10947609	1.00[CEU][hapmap];1.00[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];0.96[ASN][1000 genomes]
rs12209346	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12214285	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12215889	0.88[ASN][1000 genomes]
rs1570368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744654	0.87[ASN][1000 genomes]
rs2146333	0.83[MKK][hapmap]
rs2239807	0.82[LWK][hapmap];0.87[MKK][hapmap]
rs2300064	0.87[MKK][hapmap]
rs3752478	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3798471	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4140593	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]
rs4711450	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711452	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs515129	0.87[ASN][1000 genomes]
rs515186	0.83[ASN][1000 genomes]
rs517890	0.86[ASN][1000 genomes]
rs522179	0.88[ASN][1000 genomes]
rs544267	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs546272	0.88[ASN][1000 genomes]
rs546353	0.88[ASN][1000 genomes]
rs547026	0.90[ASN][1000 genomes]
rs547966	0.88[ASN][1000 genomes]
rs566742	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs57389119	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584196	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584418	0.88[ASN][1000 genomes]
rs595954	1.00[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];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs597153	0.88[ASN][1000 genomes]
rs600192	0.89[ASN][1000 genomes]
rs605684	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs609067	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs614028	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs619011	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs621796	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs628213	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs628314	0.88[ASN][1000 genomes]
rs629297	0.88[ASN][1000 genomes]
rs629560	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs629721	0.82[ASN][1000 genomes]
rs632943	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457918	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[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	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs664370	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs668499	0.86[CHB][hapmap]
rs6905347	0.83[MKK][hapmap]
rs6923993	1.00[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];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6926522	0.83[MKK][hapmap]
rs6927896	0.87[MKK][hapmap]
rs6941918	0.84[ASN][1000 genomes]
rs73411054	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744363	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853873	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs853881	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853882	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs860513	0.86[ASN][1000 genomes]
rs863815	0.80[ASN][1000 genomes]
rs9296183	0.81[EUR][1000 genomes]
rs9296184	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9357214	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470274	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9470278	0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs9470285	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470309	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[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
rs4711453	C6orf1	cis	parietal	SCAN
rs4711453	CPNE5	cis	cerebellum	SCAN
rs4711453	TULP1	cis	cerebellum	SCAN
rs4711453	ETV7	cis	Whole Blood	GTEx
rs4711453	PXT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36411600-36439800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:36411600-36476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:36411800-36439400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:36412200-36449200	Weak transcription	Esophagus	oesophagus
5	chr6:36412600-36449000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:36412800-36443400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:36412800-36447000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:36412800-36448600	Weak transcription	HMEC	breast
9	chr6:36419000-36449200	Weak transcription	Pancreas	Pancrea
10	chr6:36423000-36449400	Weak transcription	Gastric	stomach
11	chr6:36423400-36449600	Weak transcription	Stomach Mucosa	stomach
12	chr6:36427600-36449200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:36428600-36439400	Weak transcription	Psoas Muscle	Psoas
14	chr6:36428600-36445800	Weak transcription	Aorta	Aorta
15	chr6:36428800-36442000	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:36428800-36456600	Weak transcription	Right Atrium	heart
17	chr6:36429800-36449200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:36430000-36444600	Weak transcription	Fetal Heart	heart
19	chr6:36430000-36446000	Weak transcription	HUVEC	blood vessel
20	chr6:36430800-36488800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:36431200-36453600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:36431600-36439800	Weak transcription	NHEK	skin
23	chr6:36431600-36447600	Weak transcription	Brain Angular Gyrus	brain
24	chr6:36431600-36449000	Weak transcription	Small Intestine	intestine
25	chr6:36431600-36449200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:36431800-36449000	Weak transcription	A549	lung
27	chr6:36432000-36446800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:36432400-36449000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:36432400-36449200	Weak transcription	NHDF-Ad	bronchial
30	chr6:36432600-36439400	Weak transcription	Brain Germinal Matrix	brain
31	chr6:36433800-36449200	Weak transcription	NHLF	lung
32	chr6:36436400-36441800	Strong transcription	HSMM	muscle
33	chr6:36436400-36448800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:36436800-36452400	Weak transcription	Fetal Brain Male	brain
35	chr6:36437000-36450400	Strong transcription	Dnd41	blood
36	chr6:36437200-36440200	Strong transcription	HepG2	liver
37	chr6:36437200-36440600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:36437200-36440600	Strong transcription	GM12878-XiMat	blood
39	chr6:36437200-36449400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:36437200-36455600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:36437200-36461400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:36437400-36446200	Weak transcription	Fetal Kidney	kidney
43	chr6:36437600-36440200	Strong transcription	Primary T cells from cord blood	blood
44	chr6:36437600-36440200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:36437600-36440600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:36437600-36440600	Strong transcription	Hela-S3	cervix
47	chr6:36437600-36441400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:36437800-36440000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:36437800-36440000	Strong transcription	Right Ventricle	heart
50	chr6:36437800-36440000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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