Variant report

Variant	rs3786874
Chromosome Location	chr19:38758942-38758943
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
2	chr19:38757716..38759532-chr19:38810909..38812505,2	MCF-7	breast:
3	chr19:38756224..38759208-chr19:38851853..38853767,2	MCF-7	breast:
4	chr19:38753341..38760825-chr19:38779856..38783291,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167645	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000167642	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11083454	0.81[TSI][hapmap]
rs11538289	0.81[TSI][hapmap]
rs12610606	0.88[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs17526161	0.93[ASN][1000 genomes]
rs2074981	0.81[TSI][hapmap]
rs2286549	0.86[CHD][hapmap]
rs34276782	0.81[AFR][1000 genomes]
rs35029752	0.81[AFR][1000 genomes]
rs3745963	0.81[TSI][hapmap]
rs3760884	0.81[TSI][hapmap]
rs3786875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508781	0.82[YRI][hapmap]
rs71354994	0.81[AFR][1000 genomes]
rs7248540	0.81[TSI][hapmap]
rs7248780	0.81[TSI][hapmap]
rs7259936	0.88[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs73037307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73037309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108440	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38754600-38759000	Active TSS	Rectal Smooth Muscle	rectum
2	chr19:38755600-38760600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:38755800-38760600	Enhancers	K562	blood
4	chr19:38755800-38765200	Weak transcription	Right Atrium	heart
5	chr19:38756000-38761000	Weak transcription	HSMMtube	muscle
6	chr19:38756200-38759400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:38756200-38759400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr19:38756600-38759000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:38756600-38759000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
10	chr19:38756600-38760000	Enhancers	Stomach Mucosa	stomach
11	chr19:38756600-38772600	Weak transcription	Primary T cells from cord blood	blood
12	chr19:38756600-38772600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:38756800-38759000	Flanking Active TSS	Fetal Intestine Large	intestine
14	chr19:38756800-38759600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr19:38756800-38760800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr19:38756800-38761000	Weak transcription	Brain Anterior Caudate	brain
17	chr19:38756800-38761400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr19:38756800-38772600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr19:38756800-38774800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:38756800-38775000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:38756800-38778600	Weak transcription	Thymus	Thymus
22	chr19:38756800-38779600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:38757000-38761000	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:38757000-38761000	Weak transcription	Fetal Muscle Leg	muscle
25	chr19:38757400-38759000	Flanking Active TSS	HMEC	breast
26	chr19:38757400-38759400	Enhancers	Spleen	Spleen
27	chr19:38757400-38759600	Transcr. at gene 5' and 3'	NHEK	skin
28	chr19:38757400-38759800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr19:38757600-38759400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:38757600-38759400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:38757800-38759400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:38757800-38759400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:38757800-38759400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr19:38757800-38759400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr19:38757800-38759600	Enhancers	Fetal Brain Male	brain
36	chr19:38758000-38759000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr19:38758000-38759000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr19:38758000-38759000	Enhancers	Fetal Kidney	kidney
39	chr19:38758000-38759200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr19:38758000-38759200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr19:38758000-38759400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr19:38758000-38759800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:38758000-38759800	Flanking Active TSS	A549	lung
44	chr19:38758000-38760000	Enhancers	Hela-S3	cervix
45	chr19:38758000-38760600	Enhancers	Placenta	Placenta
46	chr19:38758000-38760800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:38758000-38761200	Weak transcription	Fetal Thymus	thymus
48	chr19:38758000-38765200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:38758000-38765200	Weak transcription	Small Intestine	intestine
50	chr19:38758000-38770800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links