Variant report

Variant	rs55641696
Chromosome Location	chr15:40627845-40627846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr15:40627649-40627899	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:40627828-40627878	ProgFib	skin:	n/a
2	chr15:40627828-40627878	HRPEpiC	eye:	n/a
3	chr15:40627828-40627878	SK-N-SH_RA	brain:	n/a
4	chr15:40627828-40627878	ECC-1	luminal epithelium:	n/a
5	chr15:40627828-40627878	GM06990	blood:	n/a
6	chr15:40627828-40627878	GM12891	blood:	n/a
7	chr15:40627828-40627878	SK-N-SH	brain:	n/a
8	chr15:40627828-40627878	HUVEC	blood vessel:	n/a
9	chr15:40627828-40627878	MCF-7	breast:	n/a
10	chr15:40627828-40627878	AG09319	gingival:	n/a
11	chr15:40627828-40627878	GM12892	blood:	n/a
12	chr15:40627828-40627878	LNCaP	prostate:	n/a
13	chr15:40627828-40627878	HAEpiC	amniotic membrane:	n/a
14	chr15:40627828-40627878	HIPEpiC	eye:	n/a
15	chr15:40627828-40627878	Jurkat	blood:	n/a
16	chr15:40627828-40627878	GM12878	blood:	n/a
17	chr15:40627828-40627878	HCM	heart:	n/a
18	chr15:40627828-40627878	CMK	blood:	n/a
19	chr15:40627828-40627878	GM19239	blood:	n/a
20	chr15:40627828-40627878	Hepatocyte	liver:	n/a
21	chr15:40627828-40627878	Caco-2	colon:	n/a
22	chr15:40627828-40627878	K562	blood:	n/a
23	chr15:40627828-40627878	HCT-116	colon:	n/a
24	chr15:40627828-40627878	MCF10A-Er-Src	breast:	n/a
25	chr15:40627828-40627878	HRE	kidney:	n/a
26	chr15:40627828-40627878	T-47D	breast:	n/a
27	chr15:40627828-40627878	HCPEpiC	choroid plexus:	n/a
28	chr15:40627828-40627878	HepG2	liver:	n/a
29	chr15:40627828-40627878	NHBE	bronchial:	n/a
30	chr15:40627828-40627878	PFSK-1	brain:	n/a
31	chr15:40627828-40627878	HL-60	blood:	n/a
32	chr15:40627828-40627878	U87	brain:	n/a
33	chr15:40627828-40627878	HRCEpiC	kidney:	n/a
34	chr15:40627828-40627878	PrEC	prostate:	n/a
35	chr15:40627828-40627878	HPAEpiC	pulmonary alveolar:	n/a
36	chr15:40627828-40627878	RPTEC	kidney:	n/a
37	chr15:40627828-40627878	ovcar-3	ovarian:	n/a
38	chr15:40627828-40627878	NT2-D1	testis:	n/a
39	chr15:40627828-40627878	AG04449	skin:	fetal
40	chr15:40627828-40627878	HMEC	breast:	n/a
41	chr15:40627828-40627878	NB4	blood:	n/a
42	chr15:40627828-40627878	AG09309	skin:	n/a
43	chr15:40627828-40627878	AG10803	skin:	n/a
44	chr15:40627828-40627878	IMR90	lung:	fetal
45	chr15:40627828-40627878	NHDF-neo	bronchial:	n/a
46	chr15:40627828-40627878	PANC-1	pancreas:	n/a
47	chr15:40627828-40627878	SK-N-MC	brain:	n/a
48	chr15:40627828-40627878	BJ	skin:	n/a
49	chr15:40627828-40627878	SAEC	small airway:	n/a
50	chr15:40627828-40627878	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type
1	chr15:40581375..40582268-chr15:40627130..40627939,2	MCF-7	breast:
2	chr15:40626383..40628344-chr15:40677759..40680121,2	K562	blood:
3	chr15:40574526..40575298-chr15:40627559..40628254,2	K562	blood:
4	chr15:40626473..40628629-chr15:40636681..40638741,2	K562	blood:
5	chr15:40589867..40591704-chr15:40625976..40628292,2	MCF-7	breast:
6	chr15:40619706..40623827-chr15:40624940..40628910,6	MCF-7	breast:
7	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
8	chr15:40612389..40614304-chr15:40626844..40628895,2	K562	blood:
9	chr15:40625172..40629583-chr15:40631432..40633911,6	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP392	TF binding region
RNA5SP392	CpG island
ENSG00000230778	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000188549	Chromatin interaction
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11630891	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634644	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17670483	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2118959	0.93[EUR][1000 genomes]
rs28602975	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62017974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731500	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72733403	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40617200-40630200	Weak transcription	A549	lung
2	chr15:40618400-40628200	Weak transcription	Brain Germinal Matrix	brain
3	chr15:40619600-40630400	Enhancers	Primary hematopoietic stem cells	blood
4	chr15:40620400-40628200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:40620800-40629600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:40621000-40630200	Weak transcription	HepG2	liver
7	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
8	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
9	chr15:40621400-40629800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:40622400-40633800	Enhancers	Spleen	Spleen
11	chr15:40622800-40628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:40623000-40629400	Weak transcription	Brain Substantia Nigra	brain
13	chr15:40623000-40630600	Weak transcription	Aorta	Aorta
14	chr15:40623200-40628200	Weak transcription	Brain Anterior Caudate	brain
15	chr15:40623200-40629600	Weak transcription	Ovary	ovary
16	chr15:40623200-40630200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:40623400-40630200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:40623800-40630600	Enhancers	Fetal Thymus	thymus
19	chr15:40624200-40630400	Weak transcription	Brain Angular Gyrus	brain
20	chr15:40624200-40630600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:40624600-40628600	Enhancers	Right Atrium	heart
22	chr15:40625000-40629600	Genic enhancers	Fetal Muscle Leg	muscle
23	chr15:40625200-40628200	Enhancers	HUVEC	blood vessel
24	chr15:40625800-40628000	Enhancers	Esophagus	oesophagus
25	chr15:40625800-40628200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr15:40625800-40628600	Enhancers	Fetal Lung	lung
27	chr15:40625800-40629200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:40625800-40630000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:40625800-40630400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:40625800-40630600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr15:40625800-40630600	Enhancers	NHDF-Ad	bronchial
32	chr15:40625800-40631600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr15:40625800-40642800	Enhancers	Fetal Intestine Large	intestine
34	chr15:40626000-40628200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr15:40626000-40628400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:40626000-40628600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:40626000-40628600	Genic enhancers	HMEC	breast
38	chr15:40626000-40628800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:40626000-40629400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:40626000-40630000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr15:40626400-40628000	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr15:40626400-40628800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:40626400-40629600	Genic enhancers	Pancreas	Pancrea
44	chr15:40626400-40629800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:40626400-40629800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr15:40626400-40629800	Weak transcription	Psoas Muscle	Psoas
47	chr15:40626400-40630400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:40626400-40631600	Enhancers	Adipose Nuclei	Adipose
49	chr15:40626600-40630000	Weak transcription	Fetal Brain Male	brain
50	chr15:40626600-40630000	Genic enhancers	Fetal Stomach	stomach

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