Variant report

Variant	rs11252861
Chromosome Location	chr10:5024394-5024395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5023921..5025963-chr10:5094008..5095926,2	MCF-7	breast:
2	chr10:5023796..5026040-chr10:5031260..5032791,2	K562	blood:
3	chr10:4891514..4892562-chr10:5023687..5025924,15	MCF-7	breast:
4	chr10:4891535..4892324-chr10:5023515..5024836,4	MCF-7	breast:
5	chr10:4911007..4912573-chr10:5023921..5026705,2	K562	blood:
6	chr10:4857646..4858298-chr10:5023972..5024754,3	MCF-7	breast:
7	chr10:5023813..5025849-chr10:5137556..5139143,2	K562	blood:
8	chr10:4867291..4868823-chr10:5022590..5025405,2	K562	blood:
9	chr10:5024232..5024860-chr10:5325292..5325936,2	K562	blood:
10	chr10:4891591..4892354-chr10:5023997..5025273,3	K562	blood:
11	chr10:4893212..4893987-chr10:5023967..5024540,4	MCF-7	breast:
12	chr10:5022739..5024559-chr10:5026616..5029182,2	K562	blood:
13	chr10:5024162..5026644-chr10:5236522..5238758,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKR1C3-4	chr10:5022258-5025472	NONHSAT011123

No data

Variant related genes	Relation type
ENSG00000198610	Chromatin interaction
ENSG00000165568	Chromatin interaction
ENSG00000196139	Chromatin interaction
ENSG00000251909	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12264914	1.00[CHB][hapmap]
rs12774134	1.00[JPT][hapmap]
rs1937859	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3890593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3923936	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4332428	1.00[JPT][hapmap]
rs4344395	1.00[JPT][hapmap]
rs4397735	1.00[JPT][hapmap]
rs4445550	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6650153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7068923	1.00[JPT][hapmap]
rs7076886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7908994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7909151	1.00[JPT][hapmap]
rs7915365	1.00[JPT][hapmap]
rs7916500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7916644	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv894794	chr10:4972761-5121745	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv430122	chr10:4986040-5134511	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv825221	chr10:4999349-5046239	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11252861	PFKP	cis	cerebellum	SCAN
rs11252861	AKR1C2	cis	multi-tissue	Pritchard
rs11252861	ATP5C1	cis	parietal	SCAN
rs11252861	tAKR	cis	cerebellum	SCAN
rs11252861	AK095239	cis	multi-tissue	Pritchard

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5005800-5027400	Weak transcription	Fetal Stomach	stomach
2	chr10:5005800-5045800	Weak transcription	HSMMtube	muscle
3	chr10:5008200-5044000	Weak transcription	Fetal Brain Male	brain
4	chr10:5009400-5027200	Weak transcription	Spleen	Spleen
5	chr10:5009600-5027000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:5011600-5044200	Weak transcription	Fetal Brain Female	brain
7	chr10:5011800-5027000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr10:5011800-5043800	Weak transcription	Psoas Muscle	Psoas
9	chr10:5012000-5027000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:5019400-5044600	Weak transcription	Brain Germinal Matrix	brain
11	chr10:5021600-5032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:5021800-5044400	Weak transcription	NHDF-Ad	bronchial
13	chr10:5023200-5024800	Enhancers	Fetal Intestine Large	intestine
14	chr10:5023600-5024400	Enhancers	HepG2	liver
15	chr10:5023600-5024800	Enhancers	Fetal Intestine Small	intestine
16	chr10:5023600-5025400	Enhancers	Fetal Muscle Leg	muscle
17	chr10:5023800-5024400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:5023800-5024400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr10:5023800-5024400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr10:5023800-5024400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr10:5023800-5024400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr10:5023800-5024400	Enhancers	Primary hematopoietic stem cells	blood
23	chr10:5023800-5024400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:5023800-5024400	Enhancers	Colon Smooth Muscle	Colon
25	chr10:5023800-5024400	Genic enhancers	Esophagus	oesophagus
26	chr10:5023800-5024400	Enhancers	Fetal Lung	lung
27	chr10:5023800-5024400	Enhancers	Ovary	ovary
28	chr10:5023800-5024400	Enhancers	Right Atrium	heart
29	chr10:5023800-5024400	Flanking Active TSS	K562	blood
30	chr10:5023800-5024600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr10:5023800-5024600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr10:5023800-5024600	Enhancers	Gastric	stomach
33	chr10:5023800-5024600	Enhancers	Thymus	Thymus
34	chr10:5023800-5024600	Flanking Active TSS	Hela-S3	cervix
35	chr10:5023800-5024800	Enhancers	H1 Cell Line	embryonic stem cell
36	chr10:5023800-5024800	Enhancers	Left Ventricle	heart
37	chr10:5023800-5024800	Flanking Active TSS	A549	lung
38	chr10:5023800-5025000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr10:5023800-5025400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr10:5023800-5025400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr10:5023800-5025400	Enhancers	Placenta	Placenta
42	chr10:5023800-5025400	Enhancers	Right Ventricle	heart
43	chr10:5023800-5025600	Enhancers	Adipose Nuclei	Adipose
44	chr10:5023800-5027800	Enhancers	Pancreas	Pancrea
45	chr10:5024000-5024400	Enhancers	H9 Cell Line	embryonic stem cell
46	chr10:5024000-5024400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr10:5024000-5024400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr10:5024000-5024400	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr10:5024000-5024400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:5024000-5024400	Enhancers	Brain Inferior Temporal Lobe	brain

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