Variant report

Variant	rs10913129
Chromosome Location	chr1:171458250-171458251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171452969..171454844-chr1:171456792..171458676,3	K562	blood:
2	chr1:171454829..171458429-chr1:171468344..171472224,4	MCF-7	breast:
3	chr1:171458059..171459731-chr1:171710164..171712290,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117523	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12124034	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12126218	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12126599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12134052	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12136219	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12145006	0.81[CEU][hapmap];0.88[AMR][1000 genomes]
rs12145591	0.88[AMR][1000 genomes]
rs12146098	0.81[CEU][hapmap];0.88[AMR][1000 genomes]
rs12403390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387832	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17586576	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17646340	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6425276	0.81[CEU][hapmap];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10913129	KLHL20	cis	parietal	SCAN
rs10913129	BRP44	cis	parietal	SCAN
rs10913129	DNM3	cis	cerebellum	SCAN
rs10913129	TNFSF18	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171455600-171461600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:171455800-171459000	Enhancers	Stomach Mucosa	stomach
3	chr1:171455800-171461600	Weak transcription	Gastric	stomach
4	chr1:171455800-171465400	Weak transcription	Lung	lung
5	chr1:171455800-171467800	Weak transcription	Spleen	Spleen
6	chr1:171456000-171459000	Weak transcription	Pancreas	Pancrea
7	chr1:171456000-171481800	Weak transcription	Placenta	Placenta
8	chr1:171456200-171459800	Enhancers	Fetal Heart	heart
9	chr1:171456200-171461600	Weak transcription	Left Ventricle	heart
10	chr1:171456200-171467800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:171456200-171475000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:171456400-171458400	Enhancers	Brain Hippocampus Middle	brain
13	chr1:171456400-171458400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:171456400-171459000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:171456400-171460200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:171456400-171460200	Enhancers	Liver	Liver
17	chr1:171456400-171460600	Enhancers	Colon Smooth Muscle	Colon
18	chr1:171456400-171461600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:171456400-171462400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:171456400-171462400	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:171456400-171466000	Weak transcription	Fetal Intestine Small	intestine
22	chr1:171456400-171467200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:171456400-171467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:171456400-171468400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:171456400-171470200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:171456400-171471200	Weak transcription	Thymus	Thymus
27	chr1:171456400-171473000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:171456400-171481800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:171456400-171483600	Weak transcription	Fetal Intestine Large	intestine
30	chr1:171456600-171458400	Enhancers	Brain Anterior Caudate	brain
31	chr1:171456600-171459000	Genic enhancers	Hela-S3	cervix
32	chr1:171456600-171460200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:171456600-171460200	Weak transcription	NHDF-Ad	bronchial
34	chr1:171456600-171460400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:171456600-171461600	Weak transcription	Psoas Muscle	Psoas
36	chr1:171456600-171467000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:171456600-171469600	Weak transcription	Fetal Stomach	stomach
38	chr1:171456800-171458400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:171456800-171458600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr1:171456800-171464200	Weak transcription	Fetal Brain Male	brain
41	chr1:171456800-171474800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:171457000-171458400	Enhancers	Adipose Nuclei	Adipose
43	chr1:171457000-171459400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:171457000-171459800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:171457000-171464000	Weak transcription	Fetal Kidney	kidney
46	chr1:171457000-171465800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr1:171457200-171459200	Genic enhancers	Primary B cells from cord blood	blood
48	chr1:171457200-171462000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:171457200-171469000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:171457400-171458400	Enhancers	Primary T helper cells fromperipheralblood	blood

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