Variant report

Variant	rs2171313
Chromosome Location	chr15:40078463-40078464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:40078463-40078481	ProgFib	skin:	n/a	n/a
2	CTCF	chr15:40078340-40078490	HEEpiC	esophagus:	n/a	n/a
3	CTCF	chr15:40078285-40079323	SK-N-SH	brain:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883
4	CTCF	chr15:40078360-40078510	HRPEpiC	eye:	n/a	n/a
5	CTCF	chr15:40078440-40078590	AG09319	gingival:	n/a	n/a
6	SMC3	chr15:40078439-40079486	SK-N-SH	brain:	n/a	chr15:40078869-40078883
7	MXI1	chr15:40078042-40079315	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr15:40078461-40079761	SK-N-SH	brain:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
9	CTCF	chr15:40078420-40078570	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:39877336..39879438-chr15:40075503..40079395,4	MCF-7	breast:
2	chr15:39981160..39982810-chr15:40077322..40078856,2	K562	blood:
3	chr15:40078363..40080929-chr15:40268662..40270401,2	MCF-7	breast:
4	chr15:40076890..40079993-chr15:40222713..40226528,3	K562	blood:
5	chr15:40078097..40078834-chr16:3355403..3356168,2	MCF-7	breast:
6	chr15:39873007..39875919-chr15:40078387..40080697,2	MCF-7	breast:
7	chr15:40077135..40079271-chr15:40079393..40081898,2	MCF-7	breast:
8	chr15:40077399..40079202-chr15:40164859..40166897,2	MCF-7	breast:
9	chr15:40051644..40053868-chr15:40078451..40080226,2	MCF-7	breast:

Variant related genes	Relation type
FSIP1	TF binding region
ENSG00000162086	Chromatin interaction
ENSG00000137801	Chromatin interaction
ENSG00000128829	Chromatin interaction
ENSG00000140993	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16969843	0.90[AFR][1000 genomes]
rs16969863	0.90[AFR][1000 genomes]
rs56933828	0.90[AFR][1000 genomes]
rs57014511	0.90[AFR][1000 genomes]
rs57761246	0.90[AFR][1000 genomes]
rs58280876	0.90[AFR][1000 genomes]
rs58766307	0.90[AFR][1000 genomes]
rs59701034	0.90[AFR][1000 genomes]
rs60642936	0.90[AFR][1000 genomes]
rs7166188	1.00[AMR][1000 genomes]
rs74008875	1.00[AFR][1000 genomes]
rs74008885	0.90[AFR][1000 genomes]
rs74008889	0.90[AFR][1000 genomes]

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	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40075800-40078600	Weak transcription	Left Ventricle	heart
2	chr15:40075800-40078800	Enhancers	Fetal Brain Male	brain
3	chr15:40075800-40079400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:40075800-40080600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:40076000-40079600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:40076000-40080600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:40076000-40081000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:40076000-40103200	Weak transcription	Right Atrium	heart
9	chr15:40076200-40078800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr15:40076200-40079800	Weak transcription	Pancreas	Pancrea
11	chr15:40076200-40080000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:40076200-40080800	Weak transcription	Primary B cells from cord blood	blood
13	chr15:40076200-40081400	Weak transcription	Fetal Kidney	kidney
14	chr15:40076400-40078600	Weak transcription	Liver	Liver
15	chr15:40076400-40078800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:40076400-40079000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr15:40076400-40079200	Enhancers	Hela-S3	cervix
18	chr15:40076400-40080600	Weak transcription	Thymus	Thymus
19	chr15:40076600-40078600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:40076600-40078600	Weak transcription	A549	lung
21	chr15:40076600-40078600	Weak transcription	HepG2	liver
22	chr15:40076600-40079000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:40076600-40079400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:40076600-40079800	Weak transcription	Fetal Thymus	thymus
25	chr15:40076600-40080000	Enhancers	HMEC	breast
26	chr15:40076600-40080200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:40076600-40080600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:40076600-40080600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:40076600-40081600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:40076600-40082000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:40076600-40082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:40076600-40082600	Weak transcription	Primary T cells from cord blood	blood
33	chr15:40076600-40084200	Weak transcription	Adipose Nuclei	Adipose
34	chr15:40076600-40086200	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:40076600-40090200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:40076600-40092600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:40076800-40078600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:40076800-40078800	Enhancers	HUVEC	blood vessel
39	chr15:40076800-40082200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr15:40076800-40082400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:40077000-40078600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:40077000-40078800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:40077200-40078600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:40077200-40078600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:40077200-40079000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr15:40077200-40079800	Weak transcription	HSMMtube	muscle
47	chr15:40077200-40081200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr15:40077200-40082600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:40077200-40082600	Enhancers	NHLF	lung
50	chr15:40077200-40092600	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links