Variant report

Variant	rs1648819
Chromosome Location	chr15:42208998-42208999
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	EBF1	chr15:42208802-42209078	GM12878	blood:	n/a	n/a
2	MTA3	chr15:42208688-42209121	GM12878	blood:	n/a	n/a
3	CTCF	chr15:42208860-42209010	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42207550..42209850-chr15:42209914..42212582,2	MCF-7	breast:
2	chr15:42208548..42210300-chr15:42220851..42222621,2	K562	blood:

Variant related genes	Relation type
ENSG00000259883	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1025227	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1030417	0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1197656	1.00[EUR][1000 genomes]
rs1197676	1.00[EUR][1000 genomes]
rs1197678	1.00[EUR][1000 genomes]
rs1197695	1.00[EUR][1000 genomes]
rs1197696	1.00[EUR][1000 genomes]
rs1197698	1.00[EUR][1000 genomes]
rs1201692	1.00[EUR][1000 genomes]
rs1451047	1.00[EUR][1000 genomes]
rs1530836	1.00[EUR][1000 genomes]
rs1614205	1.00[EUR][1000 genomes]
rs1621597	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1648808	1.00[EUR][1000 genomes]
rs1648812	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1648813	0.94[AFR][1000 genomes]
rs1648820	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1668566	1.00[EUR][1000 genomes]
rs1668590	1.00[EUR][1000 genomes]
rs1668591	1.00[EUR][1000 genomes]
rs1704408	1.00[EUR][1000 genomes]
rs1704409	1.00[EUR][1000 genomes]
rs2665209	1.00[EUR][1000 genomes]
rs2724932	1.00[EUR][1000 genomes]
rs57032192	1.00[EUR][1000 genomes]
rs6493009	1.00[EUR][1000 genomes]
rs73410628	1.00[EUR][1000 genomes]
rs890497	1.00[EUR][1000 genomes]
rs890499	1.00[EUR][1000 genomes]
rs890500	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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	chr15:42187600-42209800	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:42188600-42209600	Strong transcription	NHEK	skin
4	chr15:42190200-42209800	Weak transcription	Hela-S3	cervix
5	chr15:42190400-42218600	Weak transcription	Fetal Lung	lung
6	chr15:42195800-42209000	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:42197200-42209800	Weak transcription	A549	lung
8	chr15:42197200-42210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:42197200-42210800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:42197200-42218600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:42197400-42209600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:42197400-42218600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:42198200-42212000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:42198800-42212000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:42199000-42212600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:42199200-42209000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:42200200-42209600	Weak transcription	K562	blood
18	chr15:42201200-42225400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:42201800-42210800	Weak transcription	Thymus	Thymus
20	chr15:42201800-42211000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:42201800-42211600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:42202000-42210000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:42202200-42209600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:42202200-42209600	Weak transcription	Osteobl	bone
25	chr15:42202200-42209800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr15:42202200-42210000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:42202200-42210000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:42202200-42210600	Weak transcription	HepG2	liver
29	chr15:42202200-42218400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr15:42202200-42218600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:42202200-42225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:42202800-42209800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:42203400-42209000	Strong transcription	Fetal Intestine Large	intestine
34	chr15:42204000-42210000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:42204000-42217600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:42204200-42210000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr15:42204200-42212000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:42204400-42209600	Weak transcription	Stomach Mucosa	stomach
39	chr15:42204400-42209800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:42204400-42210800	Weak transcription	Aorta	Aorta
41	chr15:42204600-42209800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:42204600-42210000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:42204600-42210000	Weak transcription	Colonic Mucosa	Colon
44	chr15:42204600-42210000	Weak transcription	Gastric	stomach
45	chr15:42204800-42209800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:42205200-42209800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:42205200-42210200	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr15:42205400-42209800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:42205600-42209800	Weak transcription	NHDF-Ad	bronchial
50	chr15:42205800-42209600	Strong transcription	Fetal Intestine Small	intestine

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