Variant report

Variant	rs926529
Chromosome Location	chr6:24687765-24687766
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	chr6:24596221..24598717-chr6:24684990..24687804,2	MCF-7	breast:
2	chr6:24683018..24685866-chr6:24687699..24690360,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000218186	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1129644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885208	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2092404	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2143337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143339	0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2223588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223589	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181238	0.82[EUR][1000 genomes]
rs3212233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35178258	0.93[EUR][1000 genomes]
rs3777664	0.90[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3822901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397216	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4712839	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712840	0.86[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6931502	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933328	0.81[CHD][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs7752101	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764633	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs926529	NKAPL	cis	cerebellum	SCAN
rs926529	KIAA0319	cis	Whole Blood	GTEx
rs926529	TDP2	cis	Muscle Skeletal	GTEx
rs926529	ACOT13	cis	cerebellum	SCAN
rs926529	TDP2	cis	Esophagus Mucosa	GTEx
rs926529	HIST1H3G	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24668200-24699800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:24668800-24691800	Weak transcription	Psoas Muscle	Psoas
3	chr6:24669000-24690400	Weak transcription	Gastric	stomach
4	chr6:24669000-24693000	Weak transcription	Primary T cells from cord blood	blood
5	chr6:24669000-24701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:24669200-24690800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:24669400-24701600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:24674200-24700000	Weak transcription	Fetal Lung	lung
9	chr6:24674600-24703400	Weak transcription	Aorta	Aorta
10	chr6:24674800-24698200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:24674800-24702200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:24674800-24702200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:24674800-24702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:24676600-24702600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:24678200-24699600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:24678200-24702600	Weak transcription	HSMMtube	muscle
17	chr6:24678800-24701200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:24678800-24701600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:24679400-24700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:24679600-24699800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:24679800-24691800	Weak transcription	Right Ventricle	heart
22	chr6:24680000-24705400	Weak transcription	Colonic Mucosa	Colon
23	chr6:24680600-24702600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:24680800-24701600	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:24681200-24705600	Weak transcription	Ovary	ovary
26	chr6:24681400-24701800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:24682400-24703000	Weak transcription	Lung	lung
28	chr6:24682800-24691000	Weak transcription	Thymus	Thymus
29	chr6:24682800-24699000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:24682800-24701800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:24682800-24702200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:24682800-24702200	Weak transcription	Fetal Stomach	stomach
33	chr6:24683000-24701400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:24683000-24702200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:24684200-24701800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:24684400-24688600	Weak transcription	Fetal Intestine Large	intestine
37	chr6:24684400-24692200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr6:24684400-24697800	Weak transcription	Fetal Heart	heart
39	chr6:24684400-24699800	Weak transcription	HepG2	liver
40	chr6:24684600-24692800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:24684600-24701200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:24684800-24698800	Weak transcription	K562	blood
43	chr6:24684800-24705400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:24684800-24705600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:24684800-24709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:24685000-24688400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:24685000-24693400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:24685000-24698200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:24685400-24698600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:24685800-24703600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links