Variant report

Variant	rs2656073
Chromosome Location	chr15:78742276-78742277
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78596669..78599489-chr15:78741246..78743647,2	K562	blood:
2	chr15:78608718..78610938-chr15:78740404..78742745,2	K562	blood:
3	chr15:78742068..78744005-chr15:78744591..78747196,2	K562	blood:
4	chr15:78728815..78732016-chr15:78740099..78743887,5	MCF-7	breast:
5	chr15:78729183..78733288-chr15:78740820..78746070,7	K562	blood:
6	chr15:78591688..78594720-chr15:78740653..78743067,3	MCF-7	breast:
7	chr15:78740565..78742425-chr15:78743943..78746196,2	MCF-7	breast:
8	chr15:78742068..78744487-chr15:78745696..78748456,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000140395	Chromatin interaction
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10851906	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072763	0.89[EUR][1000 genomes]
rs11072766	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101809	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12442456	0.81[ASN][1000 genomes]
rs16969894	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036529	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2036533	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568497	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568498	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs2568499	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656055	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656056	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2656069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656070	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2656071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656072	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28480606	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28511883	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28602670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869032	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869045	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2915695	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938671	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2938674	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2958719	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031105	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4887053	0.94[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5019044	1.00[CEU][hapmap]
rs7174190	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174348	0.86[EUR][1000 genomes]
rs924840	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958025	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672608	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9788682	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2656073	PSMA4	cis	cerebellum	SCAN
rs2656073	COX5A	cis	parietal	SCAN
rs2656073	CHRNA5	cis	cerebellum	SCAN
rs2656073	PARP6	cis	cerebellum	SCAN
rs2656073	IREB2	cis	lesional skin	skin_eQTL
rs2656073	FAH	cis	parietal	SCAN
rs2656073	IREB2	Cis_1M	lymphoblastoid	RTeQTL
rs2656073	PSMA4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78731400-78745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:78731600-78742800	Weak transcription	Esophagus	oesophagus
3	chr15:78731600-78742800	Weak transcription	Right Ventricle	heart
4	chr15:78731600-78756400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:78731600-78760200	Weak transcription	Aorta	Aorta
6	chr15:78732200-78742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:78732200-78747600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:78732400-78742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:78732400-78744400	Weak transcription	Fetal Kidney	kidney
11	chr15:78732800-78758600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:78733400-78744000	Strong transcription	Primary B cells from cord blood	blood
13	chr15:78733800-78742400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:78733800-78743400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:78734000-78743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:78734000-78747200	Weak transcription	Fetal Brain Male	brain
17	chr15:78735000-78743600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:78735800-78743000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:78735800-78744400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:78736400-78743000	Strong transcription	Hela-S3	cervix
21	chr15:78736800-78742800	Strong transcription	GM12878-XiMat	blood
22	chr15:78738600-78747400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:78738800-78747400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:78739200-78743200	Enhancers	Adipose Nuclei	Adipose
25	chr15:78739200-78745200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:78739200-78745600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:78739200-78745600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:78739200-78747600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:78739200-78748400	Weak transcription	HSMM	muscle
30	chr15:78739200-78748800	Weak transcription	HUVEC	blood vessel
31	chr15:78739200-78749600	Weak transcription	HSMMtube	muscle
32	chr15:78739200-78755200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:78739400-78745600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:78739400-78747600	Weak transcription	NHDF-Ad	bronchial
35	chr15:78739400-78747800	Weak transcription	Osteobl	bone
36	chr15:78739600-78746800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:78739600-78755200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:78740000-78743200	Enhancers	Gastric	stomach
39	chr15:78740000-78746600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:78740200-78743000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr15:78740200-78743000	Enhancers	Brain Substantia Nigra	brain
42	chr15:78740200-78743200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:78740200-78743400	Enhancers	Left Ventricle	heart
44	chr15:78740200-78744200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:78740400-78742800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:78740400-78743000	Enhancers	Liver	Liver
47	chr15:78740400-78743000	Enhancers	Placenta Amnion	Placenta Amnion
48	chr15:78740400-78753200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:78740600-78742400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr15:78740600-78742600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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