Variant report

Variant	rs16970854
Chromosome Location	chr15:40885627-40885628
allele	A/T
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	GTF3C2	chr15:40885481-40886921	K562	blood:	n/a	n/a
2	TBP	chr15:40885414-40887116	GM12878	blood:	n/a	n/a
3	YY1	chr15:40885609-40887207	SK-N-SH	brain:	n/a	chr15:40886231-40886241 chr15:40886174-40886184 chr15:40886232-40886240 chr15:40886727-40886738 chr15:40886177-40886185 chr15:40885718-40885734 chr15:40886174-40886184 chr15:40886930-40886941 chr15:40886224-40886243 chr15:40886174-40886196
4	MAX	chr15:40885533-40887023	NB4	blood:	n/a	n/a
5	ARID3A	chr15:40885221-40886584	HepG2	liver:	n/a	n/a
6	EP300	chr15:40885549-40886699	GM12878	blood:	n/a	chr15:40885823-40885837 chr15:40885728-40885742
7	SREBP2	chr15:40884989-40888011	GM12878	blood:	n/a	n/a
8	CEBPB	chr15:40885119-40886512	K562	blood:	n/a	n/a
9	HCFC1	chr15:40885326-40888020	Hela-S3	cervix:	n/a	n/a
10	GATA3	chr15:40885214-40885817	SH-SY5Y	brain:	n/a	chr15:40885788-40885798
11	RFX5	chr15:40885609-40887630	Hela-S3	cervix:	n/a	n/a
12	EP300	chr15:40885495-40887148	GM12878	blood:	n/a	chr15:40885823-40885837 chr15:40885728-40885742
13	GTF2F1	chr15:40885588-40887079	Hela-S3	cervix:	n/a	n/a
14	TBP	chr15:40885487-40886796	Hela-S3	cervix:	n/a	n/a
15	GTF3C2	chr15:40885280-40888211	Hela-S3	cervix:	n/a	n/a
16	BRCA1	chr15:40885454-40887139	Hela-S3	cervix:	n/a	n/a
17	ARID3A	chr15:40885591-40886597	K562	blood:	n/a	n/a
18	RCOR1	chr15:40885429-40887491	Hela-S3	cervix:	n/a	n/a
19	MXI1	chr15:40884963-40888435	SK-N-SH	brain:	n/a	n/a
20	GATA1	chr15:40885347-40887503	PBDE	blood:	n/a	chr15:40886312-40886322 chr15:40885788-40885798
21	MAFK	chr15:40885566-40887757	Hela-S3	cervix:	n/a	n/a
22	NRF1	chr15:40885531-40886911	SK-N-SH	brain:	n/a	chr15:40886421-40886432 chr15:40886421-40886435 chr15:40886423-40886432 chr15:40886421-40886432 chr15:40886418-40886432
23	TAL1	chr15:40885426-40886860	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40848640..40851135-chr15:40883399..40886206,2	K562	blood:
2	chr15:40885583..40887494-chr15:40985320..40988301,2	K562	blood:
3	chr15:40884808..40888126-chr15:40896275..40900248,4	K562	blood:
4	chr15:40854296..40857804-chr15:40884735..40887632,3	K562	blood:
5	chr15:40884637..40889853-chr15:40895293..40899936,6	K562	blood:

Variant related genes	Relation type
CASC5	TF binding region
ENSG00000051180	Chromatin interaction
ENSG00000128891	Chromatin interaction
ENSG00000238559	Chromatin interaction
ENSG00000245849	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10444792	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10518696	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851397	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070276	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070278	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11632319	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12442697	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12916218	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1453182	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs1530942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1530943	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16970734	0.87[EUR][1000 genomes]
rs1801320	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1869303	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2014367	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2034653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2278887	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2278889	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2290379	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2304579	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs2412528	0.87[EUR][1000 genomes]
rs2412530	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2924389	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2959535	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2959547	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3803354	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4467046	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45455000	0.80[EUR][1000 genomes]
rs45503494	0.80[EUR][1000 genomes]
rs45507396	0.80[EUR][1000 genomes]
rs45559631	0.81[EUR][1000 genomes]
rs45579836	0.80[EUR][1000 genomes]
rs45585734	0.80[EUR][1000 genomes]
rs4561439	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4923873	0.87[EUR][1000 genomes]
rs4923877	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs4923878	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4923879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924473	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924474	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924476	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924482	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924483	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5030786	0.82[EUR][1000 genomes]
rs57140606	1.00[EUR][1000 genomes]
rs57736474	0.98[EUR][1000 genomes]
rs582736	0.87[CEU][hapmap]
rs58458955	0.86[EUR][1000 genomes]
rs589650	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs59654927	0.86[EUR][1000 genomes]
rs60408076	0.82[EUR][1000 genomes]
rs607118	0.89[EUR][1000 genomes]
rs611933	0.87[CEU][hapmap]
rs61381741	0.86[EUR][1000 genomes]
rs617031	0.89[EUR][1000 genomes]
rs623187	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs624486	0.87[CEU][hapmap]
rs640919	0.89[EUR][1000 genomes]
rs6492952	0.82[EUR][1000 genomes]
rs6492953	0.94[EUR][1000 genomes]
rs6492955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs667623	0.88[JPT][hapmap]
rs7163648	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163889	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7164056	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7164166	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7164405	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7167239	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7167922	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7168913	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7168927	0.89[EUR][1000 genomes]
rs7170073	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7170327	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7170946	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73396510	0.98[EUR][1000 genomes]
rs73396515	0.98[EUR][1000 genomes]
rs8024579	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8024802	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8029208	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8032453	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8033739	0.89[EUR][1000 genomes]
rs8034726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038350	0.82[EUR][1000 genomes]
rs8040187	1.00[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8041816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs8041991	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8043197	0.89[EUR][1000 genomes]
rs896797	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs921624	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9284288	0.89[EUR][1000 genomes]
rs976402	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9783737	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40882000-40886200	Weak transcription	Lung	lung
2	chr15:40882400-40886000	Weak transcription	Brain Substantia Nigra	brain
3	chr15:40882400-40886200	Weak transcription	HMEC	breast
4	chr15:40882600-40885800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr15:40882600-40885800	Weak transcription	Primary T cells from cord blood	blood
6	chr15:40882600-40885800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:40882600-40885800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:40882600-40885800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:40882600-40886000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr15:40882600-40886000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:40882600-40886000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:40882800-40885800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:40882800-40885800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr15:40882800-40886000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:40883000-40885800	Weak transcription	Fetal Thymus	thymus
16	chr15:40883000-40885800	Weak transcription	Thymus	Thymus
17	chr15:40883000-40885800	Weak transcription	NHEK	skin
18	chr15:40883000-40886000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:40883000-40886000	Weak transcription	Liver	Liver
20	chr15:40883000-40886000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:40883000-40886000	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:40883000-40886000	Weak transcription	Osteobl	bone
23	chr15:40883200-40886000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:40883200-40886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:40883200-40886000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:40883200-40886000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:40883200-40886000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:40883200-40886200	Weak transcription	Aorta	Aorta
29	chr15:40883200-40886200	Weak transcription	Left Ventricle	heart
30	chr15:40883200-40886200	Weak transcription	Ovary	ovary
31	chr15:40883200-40886200	Weak transcription	NHLF	lung
32	chr15:40883400-40885800	Weak transcription	Primary B cells from cord blood	blood
33	chr15:40883400-40886200	Weak transcription	Right Atrium	heart
34	chr15:40883800-40886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:40883800-40886000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:40883800-40886000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:40883800-40886200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:40884000-40885800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:40884000-40886000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr15:40884000-40886000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:40884000-40886000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:40884000-40886000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:40884000-40886000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:40884000-40886000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:40884000-40886000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:40884000-40886000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:40884000-40886000	Weak transcription	Placenta	Placenta
48	chr15:40884000-40886000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:40884000-40886200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:40884000-40886200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links