Variant report

Variant	rs9496940
Chromosome Location	chr6:144675689-144675690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144674678..144677256-chr6:144679424..144681112,2	K562	blood:
2	chr6:144663406..144666040-chr6:144675220..144677140,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152818	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11970041	0.91[AMR][1000 genomes]
rs12178630	1.00[AMR][1000 genomes]
rs17073670	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2223428	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2328570	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28737224	0.91[AMR][1000 genomes]
rs6570620	1.00[AMR][1000 genomes]
rs6570621	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6902637	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6932679	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7768531	0.84[AFR][1000 genomes]
rs9321971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484866	1.00[AMR][1000 genomes]
rs9484868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484869	0.91[AMR][1000 genomes]
rs9484870	0.91[AMR][1000 genomes]
rs9496929	1.00[AMR][1000 genomes]
rs9496933	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496934	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496939	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496943	0.84[AFR][1000 genomes]
rs9496945	0.88[AFR][1000 genomes]
rs9496946	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496947	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144653200-144684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:144663200-144685800	Weak transcription	Brain Substantia Nigra	brain
3	chr6:144665400-144696400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:144668800-144681600	Weak transcription	Small Intestine	intestine
5	chr6:144670800-144691200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:144671000-144681600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:144671000-144683200	Weak transcription	Gastric	stomach
8	chr6:144671200-144692000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:144671400-144681600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:144671400-144681600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:144671800-144681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:144671800-144683200	Weak transcription	HSMM	muscle
13	chr6:144671800-144685200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:144672000-144676000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:144672000-144683200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:144672200-144676200	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:144673000-144681400	Weak transcription	Esophagus	oesophagus
18	chr6:144673200-144675800	Enhancers	Adipose Nuclei	Adipose
19	chr6:144673200-144676000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr6:144673200-144676200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:144673200-144677800	Weak transcription	Pancreas	Pancrea
22	chr6:144673200-144678400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:144673200-144679800	Weak transcription	Ovary	ovary
24	chr6:144673200-144681400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:144673200-144683000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr6:144673200-144683200	Weak transcription	Liver	Liver
27	chr6:144673200-144683200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:144673400-144676000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:144673400-144678800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr6:144673400-144678800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr6:144673400-144681400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:144673400-144681400	Weak transcription	NHEK	skin
33	chr6:144673400-144681600	Weak transcription	Right Atrium	heart
34	chr6:144673400-144683200	Weak transcription	Stomach Mucosa	stomach
35	chr6:144673400-144683400	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:144673400-144699600	Weak transcription	Fetal Stomach	stomach
37	chr6:144673800-144676000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:144673800-144676800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:144673800-144678000	Enhancers	Primary T cells from cord blood	blood
40	chr6:144673800-144681600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:144673800-144682800	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:144674200-144676600	Enhancers	Primary B cells from cord blood	blood
43	chr6:144674200-144680200	Weak transcription	HUVEC	blood vessel
44	chr6:144674200-144680600	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr6:144674200-144681600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:144674200-144683400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:144674400-144676000	Enhancers	Fetal Thymus	thymus
48	chr6:144674600-144676000	Enhancers	Right Ventricle	heart
49	chr6:144674800-144676000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr6:144674800-144676200	Genic enhancers	Primary B cells from peripheral blood	blood

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