Variant report

Variant	rs58097169
Chromosome Location	chr15:41075627-41075628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41075550-41075738	HUVEC	blood vessel:	n/a	n/a
2	GATA3	chr15:41075418-41075719	T-47D	breast:	n/a	n/a
3	POLR2A	chr15:41075624-41075717	MCF-7	breast:	n/a	n/a
4	GATA3	chr15:41075431-41075707	T-47D	breast:	n/a	n/a
5	MAZ	chr15:41075483-41075680	K562	blood:	n/a	n/a
6	RCOR1	chr15:41075538-41075657	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41054893..41058052-chr15:41074280..41078169,3	MCF-7	breast:
2	chr15:41074776..41077084-chr15:41079776..41081556,2	K562	blood:
3	chr15:41065096..41066923-chr15:41074100..41076275,2	K562	blood:
4	chr15:41073963..41081336-chr15:41133817..41139655,12	MCF-7	breast:
5	chr15:41070585..41074304-chr15:41075540..41078752,3	K562	blood:
6	chr15:41055716..41060288-chr15:41072655..41077591,4	MCF-7	breast:
7	chr15:41069195..41071599-chr15:41075080..41078053,2	MCF-7	breast:
8	chr15:41074260..41076716-chr15:41184626..41186522,2	MCF-7	breast:
9	chr15:41045980..41048614-chr15:41075006..41076562,2	K562	blood:
10	chr15:41073204..41083534-chr15:41133992..41141155,16	MCF-7	breast:

No data

Variant related genes	Relation type
DNAJC17	TF binding region
ENSG00000137880	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000261183	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10220885	1.00[EUR][1000 genomes]
rs12323939	1.00[EUR][1000 genomes]
rs16971119	1.00[EUR][1000 genomes]
rs45501094	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45571032	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45604436	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55896567	1.00[EUR][1000 genomes]
rs55906732	1.00[EUR][1000 genomes]
rs56229816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57242620	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57288992	1.00[EUR][1000 genomes]
rs58375351	1.00[EUR][1000 genomes]
rs58681580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58738238	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59508492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59528823	1.00[EUR][1000 genomes]
rs59558714	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60109064	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60111609	1.00[EUR][1000 genomes]
rs60163307	1.00[EUR][1000 genomes]
rs60578270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60822673	1.00[EUR][1000 genomes]
rs6492962	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6492963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7161941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166733	1.00[EUR][1000 genomes]
rs7167831	1.00[EUR][1000 genomes]
rs7168217	1.00[EUR][1000 genomes]
rs7169273	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7171451	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7172356	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7178058	1.00[EUR][1000 genomes]
rs7178244	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182066	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011880	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011881	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011884	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011886	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011887	1.00[EUR][1000 genomes]
rs74011888	1.00[EUR][1000 genomes]
rs74011933	1.00[EUR][1000 genomes]
rs74011936	1.00[EUR][1000 genomes]
rs8035580	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8038751	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039169	1.00[EUR][1000 genomes]
rs8039942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040579	1.00[EUR][1000 genomes]
rs8040925	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9672224	1.00[EUR][1000 genomes]
rs9744142	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41062400-41079400	Weak transcription	Right Atrium	heart
2	chr15:41062600-41079000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:41064200-41076200	Strong transcription	Fetal Intestine Small	intestine
4	chr15:41067600-41085400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:41068000-41087800	Weak transcription	Fetal Heart	heart
6	chr15:41069200-41079200	Weak transcription	A549	lung
7	chr15:41069400-41077400	Weak transcription	Stomach Mucosa	stomach
8	chr15:41069400-41077800	Weak transcription	Small Intestine	intestine
9	chr15:41069400-41079200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:41069400-41079400	Weak transcription	NHDF-Ad	bronchial
11	chr15:41069800-41077800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:41071600-41076800	Weak transcription	Psoas Muscle	Psoas
13	chr15:41071600-41077400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:41071800-41077600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:41071800-41077800	Weak transcription	Left Ventricle	heart
16	chr15:41071800-41078000	Weak transcription	HSMM	muscle
17	chr15:41071800-41078800	Weak transcription	Osteobl	bone
18	chr15:41071800-41079200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:41071800-41079200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:41071800-41079200	Weak transcription	Brain Substantia Nigra	brain
21	chr15:41072000-41077600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:41072000-41077600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:41072000-41077600	Weak transcription	HMEC	breast
24	chr15:41072000-41078800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr15:41072000-41078800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:41072000-41079000	Weak transcription	HUVEC	blood vessel
27	chr15:41072000-41079200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:41072200-41077600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:41072200-41077800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:41072200-41077800	Weak transcription	Fetal Lung	lung
31	chr15:41072200-41078800	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:41072200-41079400	Weak transcription	Brain Anterior Caudate	brain
33	chr15:41072200-41079400	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:41072200-41079400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:41072200-41079400	Weak transcription	Fetal Thymus	thymus
36	chr15:41072200-41079600	Weak transcription	Aorta	Aorta
37	chr15:41072400-41077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:41072400-41077600	Weak transcription	Placenta	Placenta
39	chr15:41072400-41077600	Weak transcription	Ovary	ovary
40	chr15:41072400-41077600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr15:41072400-41077800	Weak transcription	Gastric	stomach
42	chr15:41072400-41077800	Weak transcription	Pancreas	Pancrea
43	chr15:41072400-41077800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:41072400-41078600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:41072400-41078600	Weak transcription	Esophagus	oesophagus
46	chr15:41072400-41078600	Weak transcription	Thymus	Thymus
47	chr15:41072400-41078600	Weak transcription	Dnd41	blood
48	chr15:41072400-41078800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:41072400-41078800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:41072400-41078800	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links