Variant report

Variant	rs6495127
Chromosome Location	chr15:75194490-75194491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:75194100-75194524	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:75187739-75194836	PFSK-1	brain:	n/a	n/a
3	CTCF	chr15:75194340-75194490	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr15:75193530-75194700	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr15:75194380-75194530	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr15:75194457-75194611	HepG2	liver:	n/a	n/a
7	CTCF	chr15:75194440-75194590	GM12875	blood:	n/a	n/a
8	CTCF	chr15:75194380-75194530	WI-38	lung:	n/a	n/a
9	POLR2A	chr15:75193609-75194589	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr15:75194400-75194550	AG04450	lung:	n/a	n/a
11	POLR2A	chr15:75193727-75194815	HCT-116	colon:	n/a	n/a
12	POLR2A	chr15:75188926-75194641	U87	brain:	n/a	n/a
13	POLR2A	chr15:75193774-75194490	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr15:75193698-75194679	MCF10A-Er-Src	breast:	n/a	n/a
15	RAD21	chr15:75193661-75194555	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr15:75192283-75194573	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr15:75187473-75194577	MCF10A-Er-Src	breast:	n/a	n/a
18	RAD21	chr15:75193697-75194490	HCT-116	colon:	n/a	n/a
19	POLR2A	chr15:75191137-75195522	K562	blood:	n/a	n/a
20	POLR2A	chr15:75194249-75194498	K562	blood:	n/a	n/a
21	POLR2A	chr15:75187680-75194520	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr15:75192296-75195541	GM12878	blood:	n/a	n/a
23	CTCF	chr15:75193154-75194747	A549	lung:	n/a	n/a
24	CTCF	chr15:75194420-75194570	GM12878	blood:	n/a	n/a
25	POLR2A	chr15:75193711-75194641	U87	brain:	n/a	n/a
26	CTCF	chr15:75194340-75194490	GM12874	blood:	n/a	n/a
27	CTCF	chr15:75194420-75194570	GM12873	blood:	n/a	n/a
28	POLR2A	chr15:75193722-75194564	HepG2	liver:	n/a	n/a
29	POLR2A	chr15:75194295-75194726	HepG2	liver:	n/a	n/a
30	CTCF	chr15:75194420-75194570	HepG2	liver:	n/a	n/a
31	MTA3	chr15:75193648-75194499	GM12878	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75182023..75183146-chr15:75193618..75194575,3	K562	blood:
2	chr15:75063523..75065570-chr15:75194170..75196593,2	MCF-7	breast:
3	chr15:75194057..75196372-chr15:75204591..75207418,2	MCF-7	breast:
4	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
5	chr15:75109529..75110053-chr15:75194068..75194696,2	MCF-7	breast:
6	chr15:75163746..75165751-chr15:75191304..75195509,4	K562	blood:
7	chr15:75161914..75167776-chr15:75191644..75199761,13	MCF-7	breast:
8	chr15:75194246..75197133-chr15:75234346..75235847,2	MCF-7	breast:
9	chr15:75184487..75185396-chr15:75193713..75194528,2	MCF-7	breast:
10	chr15:75109328..75110019-chr15:75193813..75194663,2	MCF-7	breast:
11	chr15:75152181..75153683-chr15:75192918..75194576,2	K562	blood:
12	chr15:75135330..75135924-chr15:75193876..75194522,2	MCF-7	breast:
13	chr15:75133969..75135985-chr15:75193356..75196066,3	K562	blood:
14	chr15:75120959..75123170-chr15:75193396..75195091,2	MCF-7	breast:
15	chr15:75193756..75196013-chr15:75211451..75215315,3	K562	blood:
16	chr15:75191256..75201000-chr15:75228549..75233626,13	K562	blood:
17	chr11:21367506..21368468-chr15:75194217..75195102,2	MCF-7	breast:
18	chr15:75181107..75185393-chr15:75190667..75200295,16	MCF-7	breast:
19	chr15:75194037..75196796-chr15:75249908..75252544,2	K562	blood:
20	chr15:75135208..75136037-chr15:75193638..75194600,4	K562	blood:
21	chr15:75151587..75153625-chr15:75194042..75196404,2	MCF-7	breast:
22	chr11:62608979..62609485-chr15:75194013..75194520,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
FAM219B	TF binding region
ENSG00000178741	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000178802	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12442901	0.88[GIH][hapmap]
rs12906946	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12911781	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914369	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1378938	0.88[GIH][hapmap]
rs1869959	0.87[CEU][hapmap];0.81[YRI][hapmap]
rs2168519	0.85[GIH][hapmap]
rs2301249	0.85[GIH][hapmap]
rs4886615	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs4886619	0.83[GIH][hapmap]
rs4886633	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495124	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6495126	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495131	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67411922	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7085	0.88[GIH][hapmap]
rs7162232	0.85[GIH][hapmap]
rs7174968	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7176022	0.83[GIH][hapmap]
rs7180484	0.88[GIH][hapmap]
rs7495033	0.93[EUR][1000 genomes]
rs7497201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025890	0.81[AFR][1000 genomes]
rs8031937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033381	0.85[GIH][hapmap]
rs8042694	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9210	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs936228	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs936229	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs936230	0.87[CEU][hapmap];0.95[GIH][hapmap]

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	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6495127	ULK3	cis	Whole Blood	GTEx
rs6495127	C15orf17	cis	lymphoblastoid	seeQTL
rs6495127	MPI	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:75184000-75195400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:75184200-75196600	Weak transcription	Small Intestine	intestine
4	chr15:75185000-75194800	Weak transcription	Right Atrium	heart
5	chr15:75185200-75197000	Weak transcription	Fetal Heart	heart
6	chr15:75186800-75195800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:75187600-75197200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:75187800-75196600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:75187800-75196800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:75187800-75197400	Strong transcription	Fetal Thymus	thymus
11	chr15:75188000-75196000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:75188000-75196800	Strong transcription	Brain Germinal Matrix	brain
13	chr15:75188000-75197000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:75188000-75197000	Strong transcription	Fetal Brain Female	brain
15	chr15:75188000-75197600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:75188200-75195000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:75188200-75195600	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr15:75188200-75197400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:75188200-75197400	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:75188200-75197600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:75188400-75196600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:75188400-75197400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:75188400-75197400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:75188400-75197600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:75188600-75196800	Strong transcription	NHEK	skin
26	chr15:75188600-75197400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:75188600-75197400	Strong transcription	Brain Angular Gyrus	brain
28	chr15:75188800-75197400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr15:75188800-75197400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr15:75188800-75197400	Strong transcription	Osteobl	bone
31	chr15:75189200-75197400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:75189400-75194800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:75189400-75195600	Strong transcription	Psoas Muscle	Psoas
34	chr15:75189400-75197200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:75189400-75197400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:75189800-75196400	Strong transcription	HSMM	muscle
37	chr15:75190200-75197000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:75190200-75197200	Strong transcription	Lung	lung
39	chr15:75190400-75197000	Strong transcription	Hela-S3	cervix
40	chr15:75190600-75195600	Strong transcription	Right Ventricle	heart
41	chr15:75190600-75197000	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr15:75190600-75197600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:75190600-75198200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr15:75190800-75197400	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr15:75191200-75197000	Strong transcription	Rectal Smooth Muscle	rectum
46	chr15:75191200-75197000	Strong transcription	Dnd41	blood
47	chr15:75191200-75197200	Strong transcription	Brain Substantia Nigra	brain
48	chr15:75191200-75197400	Strong transcription	Placenta	Placenta
49	chr15:75191400-75195600	Genic enhancers	Adipose Nuclei	Adipose
50	chr15:75191600-75197000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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