Variant report

Variant	rs10424090
Chromosome Location	chr19:52702623-52702624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52701335..52703547-chr19:52704651..52707579,2	MCF-7	breast:
2	chr19:52692900..52696088-chr19:52702014..52707428,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105568	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10401204	1.00[AMR][1000 genomes]
rs10401416	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10401502	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402794	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403938	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403948	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405253	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406072	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406808	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409046	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409432	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410464	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410678	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412757	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414703	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10415398	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10415475	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416801	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10418737	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10418798	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420092	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10421813	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423725	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423756	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425820	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10426412	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13344188	1.00[AMR][1000 genomes]
rs13344210	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1366243	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1366244	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription 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 miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52694400-52710200	ZNF genes & repeats	A549	lung
2	chr19:52694600-52732800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:52695200-52702800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:52695200-52708400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:52695200-52711200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:52695400-52702800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:52695400-52702800	Strong transcription	NHLF	lung
8	chr19:52695400-52707600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:52695400-52732200	Strong transcription	Fetal Lung	lung
10	chr19:52695400-52733200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:52695600-52717400	Strong transcription	Primary hematopoietic stem cells	blood
12	chr19:52696000-52710800	Strong transcription	Thymus	Thymus
13	chr19:52696000-52723000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:52696000-52732200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr19:52696000-52732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:52696000-52733000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:52696200-52704600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr19:52696200-52705200	Weak transcription	Small Intestine	intestine
19	chr19:52696200-52729200	Strong transcription	Fetal Intestine Large	intestine
20	chr19:52696200-52732400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr19:52696200-52732400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:52696200-52732400	Strong transcription	Primary B cells from cord blood	blood
23	chr19:52696600-52703200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:52696800-52705600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr19:52697600-52732400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:52697600-52733200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:52697800-52702800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:52697800-52732200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:52697800-52732400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr19:52697800-52732400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr19:52697800-52732600	Strong transcription	Primary T cells from cord blood	blood
32	chr19:52697800-52733000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:52698000-52703400	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:52698000-52730400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:52698000-52732200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr19:52698000-52732200	Strong transcription	Dnd41	blood
37	chr19:52698200-52703400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:52698200-52706400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:52698200-52714400	Weak transcription	Stomach Mucosa	stomach
40	chr19:52698200-52732000	Strong transcription	GM12878-XiMat	blood
41	chr19:52698200-52732400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:52698200-52732400	Strong transcription	HepG2	liver
43	chr19:52698200-52732600	Strong transcription	Fetal Brain Female	brain
44	chr19:52698400-52732400	Strong transcription	Fetal Thymus	thymus
45	chr19:52698600-52703200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr19:52698600-52732000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:52698800-52703200	Weak transcription	Gastric	stomach
48	chr19:52698800-52732400	Strong transcription	Liver	Liver
49	chr19:52699200-52703200	Weak transcription	Right Atrium	heart
50	chr19:52699400-52704600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links