Variant report

Variant	rs28454227
Chromosome Location	chr15:75939079-75939080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr15:75939052-75939739	A549	lung:	n/a	chr15:75939345-75939371 chr15:75939351-75939365 chr15:75939345-75939371 chr15:75939348-75939369 chr15:75939355-75939368 chr15:75939345-75939371 chr15:75939351-75939365 chr15:75939345-75939371 chr15:75939345-75939371
2	MAZ	chr15:75939005-75941749	IMR90	lung:	n/a	n/a
3	MXI1	chr15:75938376-75941832	IMR90	lung:	n/a	n/a
4	POLR2A	chr15:75939069-75941427	U87	brain:	n/a	n/a
5	POLR2A	chr15:75938666-75941213	K562	blood:	n/a	n/a
6	ZNF263	chr15:75938654-75941352	HEK293-T-REx	kidney:	n/a	chr15:75940904-75940913 chr15:75940221-75940230 chr15:75941175-75941184 chr15:75940645-75940654
7	MAX	chr15:75939067-75941169	A549	lung:	n/a	n/a
8	CHD1	chr15:75938233-75943156	IMR90	lung:	n/a	chr15:75939691-75939701 chr15:75940679-75940689
9	POLR2A	chr15:75938243-75942508	IMR90	lung:	n/a	n/a
10	POLR2A	chr15:75939050-75941378	HepG2	liver:	n/a	n/a
11	CTCF	chr15:75938313-75941384	A549	lung:	n/a	chr15:75940645-75940658 chr15:75940234-75940250 chr15:75940396-75940409 chr15:75940334-75940347 chr15:75940332-75940350

No.	Distal block	Cell Line	Cell type
1	chr15:75743471..75745101-chr15:75938448..75940487,2	MCF-7	breast:
2	chr15:75659343..75661394-chr15:75938760..75940470,2	MCF-7	breast:
3	chr15:75937430..75939214-chr15:75963572..75966390,2	MCF-7	breast:
4	chr15:75938818..75940546-chr22:39916096..39918030,2	MCF-7	breast:
5	chr15:75743610..75746369-chr15:75937608..75941096,3	K562	blood:
6	chr15:75937337..75939364-chr15:75984333..75987165,2	MCF-7	breast:
7	chr15:75745174..75747419-chr15:75938210..75940203,2	MCF-7	breast:
8	chr15:75659887..75662361-chr15:75938355..75942043,7	MCF-7	breast:

Variant related genes	Relation type
SNX33	TF binding region
ENSG00000128272	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs28458273	1.00[AMR][1000 genomes]
rs60203528	1.00[AMR][1000 genomes]
rs73449225	1.00[AMR][1000 genomes]
rs8041384	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
7	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
10	nsv904391	chr15:75930757-76001654	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
12	nsv904393	chr15:75932177-76001654	Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	nsv984485	chr15:75932760-75965433	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28454227	LOC96610	trans	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75933600-75939200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:75933600-75939200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:75938400-75939400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:75938600-75939200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:75938600-75939200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr15:75938600-75939200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:75938600-75939200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr15:75938600-75939200	Enhancers	Small Intestine	intestine
9	chr15:75938600-75939400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:75938600-75939400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:75938600-75939400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:75938600-75939400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr15:75938600-75939400	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr15:75938600-75939400	Flanking Active TSS	Hela-S3	cervix
15	chr15:75938600-75939400	Flanking Active TSS	NHDF-Ad	bronchial
16	chr15:75938600-75939400	Flanking Active TSS	NHEK	skin
17	chr15:75938600-75939400	Flanking Active TSS	NHLF	lung
18	chr15:75938600-75939600	Flanking Active TSS	Colonic Mucosa	Colon
19	chr15:75938600-75939600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr15:75938600-75939600	Flanking Active TSS	Stomach Mucosa	stomach
21	chr15:75938600-75939600	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr15:75938800-75939200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:75938800-75939200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:75938800-75939200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:75938800-75939200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:75938800-75939200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:75938800-75939200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr15:75938800-75939200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:75938800-75939200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:75938800-75939200	Flanking Active TSS	Aorta	Aorta
31	chr15:75938800-75939200	Enhancers	Brain Angular Gyrus	brain
32	chr15:75938800-75939200	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr15:75938800-75939200	Bivalent Enhancer	Fetal Thymus	thymus
34	chr15:75938800-75939200	Enhancers	Gastric	stomach
35	chr15:75938800-75939200	Flanking Active TSS	Right Atrium	heart
36	chr15:75938800-75939200	Flanking Active TSS	HepG2	liver
37	chr15:75938800-75939400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:75938800-75939400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:75938800-75939400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:75938800-75939400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr15:75938800-75939400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:75938800-75939400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:75938800-75939400	Flanking Active TSS	Esophagus	oesophagus
44	chr15:75938800-75939400	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr15:75938800-75939400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr15:75938800-75939400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr15:75938800-75939400	Enhancers	Spleen	Spleen
48	chr15:75938800-75939400	Flanking Active TSS	A549	lung
49	chr15:75938800-75939400	Flanking Active TSS	NH-A	brain
50	chr15:75938800-75939400	Flanking Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links