Variant report

Variant	rs1780180
Chromosome Location	chr10:26997925-26997926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:26995580..26998397-chr10:27011031..27013187,2	K562	blood:
2	chr10:26997066..27000236-chr10:27001137..27005066,4	K562	blood:
3	chr10:26996672..26998643-chr10:27000088..27002341,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234788	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1677728	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677730	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1748353	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1748354	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1748355	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1748356	1.00[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1748357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1780179	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1780181	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1780182	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1780184	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1780192	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2448107	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2477295	0.81[EUR][1000 genomes]
rs2477297	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2477298	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2477299	0.87[ASW][hapmap];1.00[CEU][hapmap];0.98[TSI][hapmap]
rs2489581	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3118155	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56290865	0.83[ASN][1000 genomes]
rs72797950	0.91[ASN][1000 genomes]
rs7896301	0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	23 gene(s)	inside rSNPs	diseases
3	esv1798973	chr10:26968171-27001814	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv550233	chr10:26968171-27011323	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3487618	chr10:26997046-27003844	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	esv3524271	chr10:26997596-27003294	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv3426626	chr10:26997596-27003794	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
8	esv1792880	chr10:26997918-27001814	Strong transcription Genic enhancers Weak transcription Active TSS Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv1802787	chr10:26997918-27001814	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	esv1816153	chr10:26997918-27001814	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
11	esv1794325	chr10:26997925-27001814	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1780180	LOC387646	cis	cerebellum	SCAN
rs1780180	ABI1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26987600-27010400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr10:26987600-27024400	Weak transcription	Fetal Kidney	kidney
3	chr10:26987800-27010800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr10:26987800-27020400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr10:26987800-27031200	Weak transcription	NHDF-Ad	bronchial
6	chr10:26988000-27069600	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:26988200-27004600	Weak transcription	NH-A	brain
8	chr10:26988200-27009600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:26988200-27009800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:26988400-27009800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:26989400-27031000	Weak transcription	Small Intestine	intestine
12	chr10:26990400-27002400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:26990800-26998800	Strong transcription	Dnd41	blood
14	chr10:26991600-26998200	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:26991600-26998800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr10:26992000-26998800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:26993000-26998800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr10:26993000-26999000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr10:26993400-26998800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr10:26993600-26998600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr10:26993600-26998800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr10:26993800-26998000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr10:26993800-26998400	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr10:26993800-26998600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:26993800-26998800	Strong transcription	Fetal Intestine Large	intestine
26	chr10:26993800-26999000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:26994200-26998200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr10:26994200-26998200	Strong transcription	GM12878-XiMat	blood
29	chr10:26994200-26998600	Strong transcription	Primary T cells from cord blood	blood
30	chr10:26994200-26998800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:26994200-26998800	Strong transcription	Liver	Liver
32	chr10:26994200-26999800	Strong transcription	Fetal Intestine Small	intestine
33	chr10:26994200-27007800	Strong transcription	Fetal Stomach	stomach
34	chr10:26994400-26998200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr10:26994400-26998600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr10:26994400-26998800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr10:26994400-26998800	Strong transcription	Brain Germinal Matrix	brain
38	chr10:26994400-26998800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr10:26994400-26998800	Strong transcription	Left Ventricle	heart
40	chr10:26994400-27007800	Strong transcription	Thymus	Thymus
41	chr10:26994400-27010600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr10:26994400-27040800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:26994600-26998000	Strong transcription	Hela-S3	cervix
44	chr10:26994600-26998200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr10:26994600-26998200	Strong transcription	NHEK	skin
46	chr10:26994600-26998800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:26994600-26998800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:26994600-26998800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr10:26994600-26998800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr10:26994600-26998800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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