Variant report

Variant	rs10407969
Chromosome Location	chr19:36381864-36381865
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	POLR2A	chr19:36380746-36382319	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:36380214-36382133	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:36380641-36382130	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:36380063-36382277	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:36380923-36382219	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:36380917-36382179	GM12891	blood:	n/a	n/a
7	POLR2A	chr19:36380277-36382341	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:36380402-36382086	GM18505	blood:	n/a	n/a
9	POLR2A	chr19:36381717-36382100	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:36381665-36382149	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:36380493-36382162	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:36380297-36382420	GM12891	blood:	n/a	n/a
13	POLR2A	chr19:36381774-36382122	HL-60	blood:	n/a	n/a
14	MTA3	chr19:36381686-36382156	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:36381300-36381993	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:36380229-36382289	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:36381243-36382184	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:36381573-36381922	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:36380806-36382209	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36377925..36382197-chr19:36388677..36391097,3	MCF-7	breast:
2	chr19:36379784..36382461-chr19:36387954..36392218,4	MCF-7	breast:

Variant related genes	Relation type
NFKBID	TF binding region
ENSG00000167604	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10410417	0.85[YRI][hapmap]
rs10421578	1.00[MEX][hapmap];0.85[YRI][hapmap]
rs10426635	0.82[YRI][hapmap]
rs13344146	0.85[YRI][hapmap]
rs28625208	1.00[MEX][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active 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	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10407969	RNF130	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36361000-36389000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:36361200-36389200	Weak transcription	Right Atrium	heart
3	chr19:36370600-36389000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:36370800-36389200	Weak transcription	HSMM	muscle
5	chr19:36370800-36389400	Weak transcription	HUVEC	blood vessel
6	chr19:36370800-36389400	Weak transcription	NH-A	brain
7	chr19:36373400-36389600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:36373600-36389200	Weak transcription	Fetal Brain Male	brain
9	chr19:36376200-36384000	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr19:36376200-36386600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:36376400-36386000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:36376400-36388400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:36376600-36383800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:36376600-36387800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:36377200-36386600	Weak transcription	HepG2	liver
16	chr19:36377400-36387000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr19:36377600-36387000	Strong transcription	Primary T cells from cord blood	blood
18	chr19:36377600-36388800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:36377600-36388800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:36377600-36389000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:36377600-36389000	Strong transcription	Fetal Stomach	stomach
22	chr19:36377600-36389400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:36377800-36382200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:36377800-36382200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:36377800-36382400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:36377800-36382400	Strong transcription	Osteobl	bone
27	chr19:36377800-36382600	Strong transcription	A549	lung
28	chr19:36377800-36386800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:36377800-36386800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:36377800-36386800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:36377800-36386800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:36377800-36387000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr19:36377800-36387000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr19:36377800-36387600	Strong transcription	Fetal Thymus	thymus
35	chr19:36377800-36387800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:36377800-36387800	Strong transcription	Adipose Nuclei	Adipose
37	chr19:36377800-36388600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:36377800-36388600	Strong transcription	Spleen	Spleen
39	chr19:36377800-36389000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:36378000-36382200	Strong transcription	Brain Anterior Caudate	brain
41	chr19:36378000-36382200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:36378000-36382200	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:36378000-36382600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:36378000-36384000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:36378000-36385800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:36378000-36387200	Strong transcription	Thymus	Thymus
47	chr19:36378000-36388000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:36378000-36388000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:36378000-36388600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:36378200-36382400	Strong transcription	H9 Cell Line	embryonic stem cell

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