Variant report

Variant	rs16970660
Chromosome Location	chr15:40700767-40700768
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	chr15:40700767-40701153	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40700603..40702646-chr15:40703222..40705401,2	MCF-7	breast:
2	chr15:40698036..40700084-chr15:40700377..40704412,6	MCF-7	breast:

Variant related genes	Relation type
IVD	TF binding region
ENSG00000128928	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11541641	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11541643	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12185076	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16970653	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2229312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28379196	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6492944	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs68169695	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7176592	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs7177949	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs72733427	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72733428	0.94[EUR][1000 genomes]
rs72733434	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72733437	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72733442	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72733444	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72733445	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72733449	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72733450	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72733453	0.94[EUR][1000 genomes]
rs73383135	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8031814	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8031994	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8032114	1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8036457	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8037941	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs875767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs967944	1.00[YRI][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16970660	C15orf23	Cis_1M	lymphoblastoid	RTeQTL
rs16970660	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs16970660	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40698600-40702400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40698600-40702400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:40698600-40702400	Weak transcription	Aorta	Aorta
4	chr15:40698600-40702400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:40698600-40712400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:40698800-40702200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:40698800-40702400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:40698800-40702600	Weak transcription	Right Ventricle	heart
9	chr15:40698800-40702600	Weak transcription	A549	lung
10	chr15:40698800-40707000	Weak transcription	Psoas Muscle	Psoas
11	chr15:40698800-40707600	Weak transcription	NHEK	skin
12	chr15:40698800-40709600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:40699000-40701200	Weak transcription	Fetal Kidney	kidney
14	chr15:40699000-40701600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:40699000-40702200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:40699000-40702400	Weak transcription	Esophagus	oesophagus
17	chr15:40699000-40702600	Weak transcription	NH-A	brain
18	chr15:40699000-40703200	Weak transcription	Stomach Mucosa	stomach
19	chr15:40699000-40714000	Weak transcription	Small Intestine	intestine
20	chr15:40699400-40700800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:40699600-40700800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:40699600-40702400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:40699600-40703000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:40699600-40704400	Strong transcription	Adipose Nuclei	Adipose
25	chr15:40699600-40704400	Strong transcription	Fetal Intestine Small	intestine
26	chr15:40699600-40704600	Strong transcription	Fetal Lung	lung
27	chr15:40699600-40710000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:40699600-40710800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:40699600-40710800	Strong transcription	Primary T cells from cord blood	blood
30	chr15:40699600-40711000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:40699600-40711000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:40699600-40711000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:40699600-40711200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:40699600-40712400	Weak transcription	Right Atrium	heart
35	chr15:40699600-40714000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:40699800-40700800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:40699800-40701000	Strong transcription	Gastric	stomach
38	chr15:40699800-40701200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:40699800-40701400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:40699800-40701400	Strong transcription	Placenta	Placenta
41	chr15:40699800-40701800	Strong transcription	HUVEC	blood vessel
42	chr15:40699800-40702600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:40699800-40702600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:40699800-40702600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:40699800-40702600	Weak transcription	Hela-S3	cervix
46	chr15:40699800-40704400	Strong transcription	Fetal Intestine Large	intestine
47	chr15:40699800-40709000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr15:40699800-40709200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:40699800-40709200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:40699800-40710800	Strong transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links