Variant report

Variant	rs2158004
Chromosome Location	chr19:19033089-19033090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19031832-19034016	U87	brain:	n/a	n/a
2	POLR2A	chr19:19032946-19033685	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:19033010-19033210	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:19032868-19033920	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:19032712-19033219	K562	blood:	n/a	n/a
6	POLR2A	chr19:19033081-19033162	A549	lung:	n/a	n/a
7	POLR2A	chr19:19031838-19033917	U87	brain:	n/a	n/a
8	POLR2A	chr19:19032951-19033333	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:19033077-19033171	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:19031896-19034067	HL-60	blood:	n/a	n/a
11	POLR2A	chr19:19033009-19033593	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19031206..19033838-chr19:19067854..19070474,2	MCF-7	breast:
2	chr19:19028307..19038067-chr19:19048419..19054729,15	MCF-7	breast:
3	chr19:19028142..19040542-chr19:19046967..19057144,34	MCF-7	breast:

No data

Variant related genes	Relation type
DDX49	TF binding region
COPE	TF binding region
ENSG00000269019	Chromatin interaction
ENSG00000241172	Chromatin interaction
ENSG00000051128	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10330	0.81[ASW][hapmap];0.85[TSI][hapmap]
rs16995785	0.81[CEU][hapmap]
rs2106660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231993	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872205	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55988241	0.82[EUR][1000 genomes]
rs7250615	0.86[EUR][1000 genomes]
rs73003085	0.81[EUR][1000 genomes]
rs73003087	0.86[EUR][1000 genomes]
rs73003090	0.85[EUR][1000 genomes]
rs999454	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv470132	chr19:18964442-19054720	Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv911301	chr19:18994638-19077385	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911302	chr19:18995201-19088981	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv543926	chr19:19029529-19062771	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19031400-19033200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:19031400-19033200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:19031600-19033200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:19031600-19033200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr19:19031600-19033200	Weak transcription	Brain Substantia Nigra	brain
6	chr19:19031600-19033400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:19031600-19033400	Weak transcription	Stomach Mucosa	stomach
8	chr19:19031600-19033600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:19031600-19033800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:19031600-19033800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:19031600-19034000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:19031600-19034400	Weak transcription	NH-A	brain
13	chr19:19031600-19034600	Strong transcription	K562	blood
14	chr19:19031600-19035000	Weak transcription	Psoas Muscle	Psoas
15	chr19:19031600-19035200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:19031600-19035400	Weak transcription	Fetal Kidney	kidney
17	chr19:19031600-19035400	Weak transcription	Small Intestine	intestine
18	chr19:19031600-19037400	Strong transcription	NHLF	lung
19	chr19:19031600-19042600	Weak transcription	Fetal Heart	heart
20	chr19:19031600-19042600	Strong transcription	Fetal Intestine Small	intestine
21	chr19:19031600-19043200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:19031600-19043200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:19031600-19043200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:19031600-19044000	Weak transcription	HSMM	muscle
25	chr19:19031600-19045200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:19031800-19033400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:19031800-19033600	Weak transcription	Hela-S3	cervix
28	chr19:19031800-19040600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:19031800-19042800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:19031800-19043400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:19031800-19043400	Strong transcription	Fetal Stomach	stomach
32	chr19:19032000-19033400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:19032000-19037200	Strong transcription	Esophagus	oesophagus
34	chr19:19032000-19039800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr19:19032000-19039800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr19:19032000-19040000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:19032000-19040400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:19032000-19040600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:19032000-19040600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:19032000-19043000	Strong transcription	Fetal Intestine Large	intestine
41	chr19:19032000-19045600	Strong transcription	Osteobl	bone
42	chr19:19032000-19046000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:19032200-19034000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:19032200-19037400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:19032200-19037400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:19032200-19038800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:19032200-19039200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:19032200-19039400	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr19:19032200-19039600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:19032200-19040000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links