Variant report

Variant	rs60973674
Chromosome Location	chr19:19309115-19309116
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	REST	chr19:19308824-19309161	ECC-1	luminal epithelium:	n/a	chr19:19308891-19308909
2	POLR2A	chr19:19309041-19309807	K562	blood:	n/a	n/a
3	POLR2A	chr19:19309062-19309495	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:19308940-19309777	SK-N-MC	brain:	n/a	n/a
5	REST	chr19:19308862-19309185	ECC-1	luminal epithelium:	n/a	chr19:19308891-19308909

No.	Distal block	Cell Line	Cell type
1	chr19:19307535..19311874-chr19:19311949..19315894,9	MCF-7	breast:
2	chr19:19302763..19305800-chr19:19307599..19310833,3	MCF-7	breast:
3	chr19:19307070..19310712-chr19:19311051..19314432,7	MCF-7	breast:
4	chr19:19308004..19310412-chr19:19430243..19432746,2	K562	blood:
5	chr19:19299448..19305567-chr19:19306959..19319217,21	K562	blood:
6	chr19:19301788..19305469-chr19:19308325..19310505,4	K562	blood:

Variant related genes	Relation type
RFXANK	TF binding region
ENSG00000105705	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000184162	Chromatin interaction
ENSG00000064490	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56738402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57362874	0.97[AFR][1000 genomes]
rs59210450	0.85[AMR][1000 genomes]
rs60666927	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7256074	0.85[AMR][1000 genomes]
rs73922820	0.85[AMR][1000 genomes]
rs73922821	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922822	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922826	0.85[AMR][1000 genomes]
rs73922828	0.85[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	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv933613	chr19:19291456-19312244	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv961283	chr19:19293486-19312277	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19304200-19313400	Weak transcription	Fetal Kidney	kidney
2	chr19:19304200-19313400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:19304600-19312600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr19:19304800-19313000	Weak transcription	Stomach Mucosa	stomach
5	chr19:19304800-19313000	Weak transcription	HSMM	muscle
6	chr19:19304800-19313200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:19304800-19313600	Weak transcription	Small Intestine	intestine
8	chr19:19305000-19310400	Weak transcription	HUVEC	blood vessel
9	chr19:19305000-19311000	Strong transcription	Fetal Thymus	thymus
10	chr19:19305000-19312400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:19305000-19312400	Weak transcription	HepG2	liver
12	chr19:19305000-19313400	Weak transcription	Fetal Heart	heart
13	chr19:19305400-19312400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:19305400-19313200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:19305600-19309200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:19305600-19311400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:19305600-19312400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:19305600-19312800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:19305600-19313000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:19305600-19313000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:19305600-19313000	Weak transcription	Right Atrium	heart
22	chr19:19305600-19313200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:19305600-19313200	Weak transcription	Psoas Muscle	Psoas
24	chr19:19305800-19312200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:19305800-19312400	Weak transcription	Hela-S3	cervix
26	chr19:19305800-19312600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:19305800-19312600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:19305800-19313000	Strong transcription	Fetal Muscle Leg	muscle
29	chr19:19305800-19313000	Strong transcription	Fetal Stomach	stomach
30	chr19:19305800-19313200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:19306000-19311200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:19306200-19310800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr19:19306200-19310800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:19306200-19311200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr19:19306200-19311800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:19306200-19312400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:19306200-19312600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:19306600-19310600	Strong transcription	Thymus	Thymus
39	chr19:19306600-19311000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr19:19306800-19309600	Strong transcription	NHDF-Ad	bronchial
41	chr19:19306800-19310200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:19306800-19310800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:19306800-19310800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:19306800-19310800	Strong transcription	Brain Hippocampus Middle	brain
45	chr19:19306800-19311000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:19306800-19311000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:19306800-19312200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:19306800-19313000	Strong transcription	Fetal Intestine Small	intestine
49	chr19:19307000-19310000	Strong transcription	GM12878-XiMat	blood
50	chr19:19307000-19310200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links