Variant report

Variant	rs3752478
Chromosome Location	chr6:36492375-36492376
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36487982..36489782-chr6:36491211..36493166,2	K562	blood:
2	chr6:36490465..36493524-chr6:36513455..36516315,3	MCF-7	breast:
3	chr6:36491869..36493781-chr6:36501764..36503876,2	MCF-7	breast:
4	chr6:36488938..36493688-chr6:36561807..36564126,6	MCF-7	breast:
5	chr6:36492107..36493625-chr6:36501687..36504348,2	K562	blood:
6	chr6:36490205..36492952-chr6:36495728..36497599,2	MCF-7	breast:
7	chr6:36476518..36479217-chr6:36491251..36492884,2	MCF-7	breast:
8	chr6:36487455..36494660-chr6:36559051..36563997,8	MCF-7	breast:
9	chr6:36492328..36495543-chr6:36512590..36515931,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112079	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000264878	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

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];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10440841	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10947609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209346	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12214285	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12215889	0.83[ASN][1000 genomes]
rs1570368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1744654	0.82[ASN][1000 genomes]
rs2146333	0.82[MKK][hapmap]
rs2239807	0.86[MKK][hapmap]
rs2300064	0.86[MKK][hapmap]
rs3798471	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140593	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]
rs4711450	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711452	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711453	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]
rs515129	0.82[ASN][1000 genomes]
rs517890	0.81[ASN][1000 genomes]
rs522179	0.82[ASN][1000 genomes]
rs544267	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs546272	0.83[ASN][1000 genomes]
rs546353	0.83[ASN][1000 genomes]
rs547026	0.84[ASN][1000 genomes]
rs547966	0.83[ASN][1000 genomes]
rs566742	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs57389119	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs584196	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs584418	0.82[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];0.92[ASN][1000 genomes]
rs597153	0.83[ASN][1000 genomes]
rs600192	0.84[ASN][1000 genomes]
rs605684	0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs609067	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614028	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs619011	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[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];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs628314	0.83[ASN][1000 genomes]
rs629297	0.83[ASN][1000 genomes]
rs629560	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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];0.81[EUR][1000 genomes];0.88[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];0.82[ASN][1000 genomes]
rs668499	0.86[CHB][hapmap]
rs6905347	0.82[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];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6926522	0.82[MKK][hapmap]
rs6927896	0.86[MKK][hapmap]
rs6941918	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73411054	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7744363	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853873	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs853881	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853882	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs860513	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296184	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9357214	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9470274	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9470278	0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs9470285	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9470309	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv5260	chr6:36471464-36516119	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3752478	CPNE5	cis	cerebellum	SCAN
rs3752478	C6orf1	cis	parietal	SCAN
rs3752478	PXT1	cis	lymphoblastoid	seeQTL
rs3752478	ETV7	cis	Whole Blood	GTEx
rs3752478	TULP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36456400-36512600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:36463000-36507200	Weak transcription	Fetal Brain Male	brain
3	chr6:36463600-36493600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr6:36463800-36493400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr6:36463800-36513600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:36470600-36498800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:36473600-36500000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:36474000-36495200	Weak transcription	Fetal Heart	heart
9	chr6:36476200-36497800	Strong transcription	Dnd41	blood
10	chr6:36476800-36512200	Weak transcription	Brain Angular Gyrus	brain
11	chr6:36477400-36507400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr6:36478400-36493600	Weak transcription	Esophagus	oesophagus
13	chr6:36478400-36507400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:36478400-36507800	Strong transcription	Fetal Thymus	thymus
15	chr6:36478400-36513600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:36478400-36514000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:36478600-36493000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:36478800-36497400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:36478800-36512400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:36479000-36493000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:36479600-36514400	Weak transcription	Spleen	Spleen
22	chr6:36480200-36493800	Weak transcription	Stomach Mucosa	stomach
23	chr6:36480200-36496000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:36481400-36512000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:36481800-36493800	Strong transcription	HSMMtube	muscle
26	chr6:36482000-36493600	Strong transcription	Adipose Nuclei	Adipose
27	chr6:36482000-36493800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:36482000-36494000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:36482200-36493400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:36482200-36494200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:36482600-36493400	Strong transcription	Primary B cells from cord blood	blood
32	chr6:36483200-36500000	Weak transcription	Lung	lung
33	chr6:36483600-36493600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:36484000-36492600	Weak transcription	NHEK	skin
35	chr6:36484200-36493200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:36484200-36493400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:36484200-36506200	Weak transcription	Brain Substantia Nigra	brain
38	chr6:36484600-36493600	Strong transcription	Placenta	Placenta
39	chr6:36484600-36493600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr6:36484600-36507600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:36484600-36514000	Weak transcription	Pancreas	Pancrea
42	chr6:36484800-36493400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr6:36484800-36493800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr6:36484800-36512400	Weak transcription	Right Atrium	heart
45	chr6:36485800-36494200	Strong transcription	Fetal Intestine Large	intestine
46	chr6:36486000-36493800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:36486200-36493600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr6:36486600-36493400	Strong transcription	HUVEC	blood vessel
49	chr6:36486600-36493800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:36486800-36493400	Strong transcription	Stomach Smooth Muscle	stomach

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