Variant report

Variant	rs16972253
Chromosome Location	chr15:42211663-42211664
allele	C/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	POLR2A	chr15:42210672-42212000	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:42209758-42212774	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:42210611-42212076	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:42209786-42212072	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:42210650-42212167	GM12891	blood:	n/a	n/a
6	POLR2A	chr15:42211552-42211668	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr15:42209705-42212218	GM12892	blood:	n/a	n/a
8	POLR2A	chr15:42210630-42212143	GM12891	blood:	n/a	n/a
9	POLR2A	chr15:42211334-42211929	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:42210704-42212101	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42209684..42211751-chr15:42216402..42218970,2	MCF-7	breast:
2	chr15:42202438..42205069-chr15:42210826..42212891,2	MCF-7	breast:
3	chr15:42207550..42209850-chr15:42209914..42212582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259883	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12102194	1.00[EUR][1000 genomes]
rs16972234	0.89[AFR][1000 genomes]
rs16972239	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16972264	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16972274	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs16972281	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16972286	0.86[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16972405	1.00[EUR][1000 genomes]
rs17842096	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28626380	1.00[EUR][1000 genomes]
rs34424865	1.00[EUR][1000 genomes]
rs34807597	1.00[EUR][1000 genomes]
rs36126315	1.00[EUR][1000 genomes]
rs61281049	1.00[EUR][1000 genomes]
rs61736067	1.00[EUR][1000 genomes]
rs61741913	1.00[EUR][1000 genomes]
rs61748710	1.00[EUR][1000 genomes]
rs61753581	1.00[EUR][1000 genomes]
rs7173832	0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176585	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7177717	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180290	1.00[EUR][1000 genomes]
rs7182680	1.00[EUR][1000 genomes]
rs7182959	1.00[EUR][1000 genomes]
rs919142	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
5	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
6	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
7	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv976926	chr15:42202094-42217599	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
2	chr15:42190400-42218600	Weak transcription	Fetal Lung	lung
3	chr15:42197200-42218600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:42197400-42218600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:42198200-42212000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:42198800-42212000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr15:42199000-42212600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:42201200-42225400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42202200-42218400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:42202200-42218600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:42202200-42225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:42204000-42217600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:42204200-42212000	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:42208200-42212000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:42208200-42212000	Strong transcription	Primary T cells from cord blood	blood
16	chr15:42208200-42212000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:42208200-42212000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:42208400-42212000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:42208400-42212000	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr15:42208400-42212000	Genic enhancers	Fetal Muscle Leg	muscle
21	chr15:42208400-42212000	Genic enhancers	Lung	lung
22	chr15:42208400-42212800	Genic enhancers	Placenta	Placenta
23	chr15:42208400-42214400	Enhancers	Right Atrium	heart
24	chr15:42208400-42214800	Enhancers	Ovary	ovary
25	chr15:42208400-42218800	Genic enhancers	HUVEC	blood vessel
26	chr15:42208600-42211800	Weak transcription	Fetal Kidney	kidney
27	chr15:42208800-42211800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:42209200-42212000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr15:42209200-42218000	Weak transcription	Fetal Thymus	thymus
30	chr15:42209600-42213800	Genic enhancers	Fetal Intestine Small	intestine
31	chr15:42209800-42211800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr15:42209800-42211800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:42209800-42211800	Transcr. at gene 5' and 3'	Pancreas	Pancrea
34	chr15:42209800-42211800	Enhancers	Psoas Muscle	Psoas
35	chr15:42209800-42212000	Genic enhancers	NHLF	lung
36	chr15:42209800-42212400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:42209800-42212800	Genic enhancers	Spleen	Spleen
38	chr15:42209800-42216000	Strong transcription	GM12878-XiMat	blood
39	chr15:42210000-42211800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:42210000-42211800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:42210000-42211800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr15:42210000-42212000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:42210000-42212000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:42210000-42212000	Strong transcription	Colonic Mucosa	Colon
45	chr15:42210000-42212000	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr15:42210000-42212000	Genic enhancers	Gastric	stomach
47	chr15:42210000-42214400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:42210200-42211800	Strong transcription	Liver	Liver
49	chr15:42210200-42212000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:42210200-42216000	Weak transcription	Primary hematopoietic stem cells	blood

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