Variant report

Variant	rs9964979
Chromosome Location	chr18:12331501-12331502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12330971..12332498-chr18:12334634..12336451,2	K562	blood:
2	chr18:12330814..12333752-chr18:12371346..12373010,2	MCF-7	breast:
3	chr18:12329605..12332394-chr18:12338535..12341169,2	K562	blood:
4	chr18:12325110..12326750-chr18:12329700..12331543,2	K562	blood:
5	chr18:12327453..12330082-chr18:12330908..12334376,4	K562	blood:
6	chr18:12326458..12332320-chr18:12374113..12378268,7	K562	blood:

Variant related genes	Relation type
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11080566	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3786261	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap]
rs552600	1.00[YRI][hapmap]
rs62095741	0.80[AMR][1000 genomes]
rs7228252	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats 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	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active 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	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers 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	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers 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	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12312600-12332600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr18:12314000-12333600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:12314400-12342600	Weak transcription	Small Intestine	intestine
4	chr18:12316400-12333600	Weak transcription	Fetal Brain Male	brain
5	chr18:12318400-12334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:12318600-12331600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:12319000-12333800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr18:12319000-12336800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr18:12320800-12348200	Strong transcription	Fetal Intestine Small	intestine
10	chr18:12321200-12331600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr18:12321200-12331600	Strong transcription	Duodenum Mucosa	Duodenum
12	chr18:12323000-12332400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr18:12323400-12342800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr18:12324400-12331800	Strong transcription	Thymus	Thymus
15	chr18:12324600-12331600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr18:12324800-12332200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr18:12324800-12337000	Strong transcription	Liver	Liver
18	chr18:12324800-12338800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr18:12324800-12339400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr18:12325200-12335800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr18:12325800-12331600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr18:12325800-12331800	Strong transcription	Fetal Stomach	stomach
23	chr18:12325800-12332200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr18:12326000-12343200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr18:12326200-12366400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr18:12326400-12332400	Strong transcription	Fetal Intestine Large	intestine
27	chr18:12326800-12333600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr18:12326800-12334400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr18:12327000-12331600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr18:12327000-12333800	Weak transcription	Aorta	Aorta
31	chr18:12327400-12333800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr18:12327800-12334000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr18:12328000-12332000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:12328000-12333600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr18:12328000-12333800	Weak transcription	Brain Substantia Nigra	brain
36	chr18:12328000-12335400	Weak transcription	Psoas Muscle	Psoas
37	chr18:12328000-12335600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr18:12328200-12332600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:12328200-12333600	Weak transcription	Spleen	Spleen
40	chr18:12328200-12333600	Weak transcription	A549	lung
41	chr18:12328400-12334600	Weak transcription	Stomach Mucosa	stomach
42	chr18:12328800-12333600	Weak transcription	Fetal Heart	heart
43	chr18:12328800-12333800	Weak transcription	Esophagus	oesophagus
44	chr18:12328800-12333800	Weak transcription	HSMMtube	muscle
45	chr18:12329200-12331600	Strong transcription	Right Ventricle	heart
46	chr18:12329200-12333600	Weak transcription	Fetal Kidney	kidney
47	chr18:12329400-12331600	Strong transcription	Left Ventricle	heart
48	chr18:12329400-12332200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr18:12329400-12332200	Strong transcription	Fetal Muscle Leg	muscle
50	chr18:12329600-12333400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links