Variant report

Variant	rs35016410
Chromosome Location	chr19:44019419-44019420
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44008047..44009718-chr19:44018609..44021127,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176531	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12460021	0.86[EUR][1000 genomes]
rs12979907	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12980646	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12981023	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs184239	0.81[EUR][1000 genomes]
rs1978008	0.81[EUR][1000 genomes]
rs2102954	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2682585	0.82[EUR][1000 genomes]
rs2854506	0.82[EUR][1000 genomes]
rs2854507	0.81[EUR][1000 genomes]
rs2854508	0.82[EUR][1000 genomes]
rs2854509	0.82[EUR][1000 genomes]
rs304731	0.81[EUR][1000 genomes]
rs3213295	0.81[EUR][1000 genomes]
rs3213391	0.85[EUR][1000 genomes]
rs34977009	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35485252	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36075334	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3810381	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4507015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4544340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802183	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4802185	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59000923	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59827264	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61607741	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6509094	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71362654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248927	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252962	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253177	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs762506	0.82[EUR][1000 genomes]
rs8100211	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35016410	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL
rs35016410	ETHE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44009000-44023600	Weak transcription	Stomach Mucosa	stomach
2	chr19:44009200-44029200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:44009200-44029600	Weak transcription	Psoas Muscle	Psoas
4	chr19:44009400-44020200	Weak transcription	Right Atrium	heart
5	chr19:44009400-44022000	Weak transcription	Primary B cells from cord blood	blood
6	chr19:44009400-44023600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:44009600-44023400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:44009600-44023600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:44009600-44023600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:44009800-44019800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:44009800-44021600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:44010000-44021800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:44010200-44021600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:44010200-44023400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr19:44010400-44023000	Weak transcription	Hela-S3	cervix
16	chr19:44010400-44023400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:44010400-44023600	Weak transcription	K562	blood
18	chr19:44011200-44029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:44012800-44021600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:44013000-44028600	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:44013000-44028800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:44013200-44020000	Weak transcription	HSMM	muscle
23	chr19:44013200-44023400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:44013200-44028600	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:44013200-44029800	Weak transcription	Small Intestine	intestine
26	chr19:44013400-44023000	Weak transcription	NH-A	brain
27	chr19:44013400-44023800	Weak transcription	Fetal Lung	lung
28	chr19:44013400-44029400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:44013600-44023600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:44014400-44023200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:44014400-44023400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:44014400-44029400	Weak transcription	Dnd41	blood
33	chr19:44015000-44023000	Weak transcription	HSMMtube	muscle
34	chr19:44015200-44021000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:44015200-44028600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr19:44015200-44028800	Weak transcription	Gastric	stomach
37	chr19:44015400-44023400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:44015400-44023600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:44015400-44028400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:44015400-44028800	Weak transcription	Fetal Thymus	thymus
41	chr19:44015400-44028800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:44015400-44029000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:44015400-44029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:44015400-44029400	Weak transcription	Brain Germinal Matrix	brain
45	chr19:44015400-44029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:44015600-44021800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr19:44015600-44021800	Weak transcription	Placenta	Placenta
48	chr19:44015600-44022000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:44015600-44023000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:44015600-44023000	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links