Variant report

Variant	rs34664675
Chromosome Location	chr15:77708932-77708933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr15:77708555-77709036	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr15:77708852-77709282	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:77708914-77708964	A549	lung:	n/a
2	chr15:77708914-77708964	K562	blood:	n/a
3	chr15:77708914-77708964	HNPCEpiC	eye:	n/a
4	chr15:77708914-77708964	NHBE	bronchial:	n/a
5	chr15:77708914-77708964	AoSMC	blood vessel:	n/a
6	chr15:77708914-77708964	HCF	heart:	n/a
7	chr15:77708914-77708964	AG09319	gingival:	n/a
8	chr15:77708914-77708964	HMEC	breast:	n/a
9	chr15:77708914-77708964	HL-60	blood:	n/a
10	chr15:77708914-77708964	GM12891	blood:	n/a
11	chr15:77708914-77708964	HEK293	kidney:	embryo
12	chr15:77708914-77708964	HCM	heart:	n/a
13	chr15:77708914-77708964	PrEC	prostate:	n/a
14	chr15:77708914-77708964	AG09309	skin:	n/a
15	chr15:77708914-77708964	HCPEpiC	choroid plexus:	n/a
16	chr15:77708914-77708964	HPAEpiC	pulmonary alveolar:	n/a
17	chr15:77708914-77708964	MCF10A-Er-Src	breast:	n/a
18	chr15:77708914-77708964	ovcar-3	ovarian:	n/a
19	chr15:77708914-77708964	RPTEC	kidney:	n/a
20	chr15:77708914-77708964	AG10803	skin:	n/a
21	chr15:77708914-77708964	NH-A	brain:	n/a
22	chr15:77708914-77708964	LNCaP	prostate:	n/a
23	chr15:77708914-77708964	SKMC	muscle:	n/a
24	chr15:77708914-77708964	NT2-D1	testis:	n/a
25	chr15:77708914-77708964	GM12892	blood:	n/a
26	chr15:77708914-77708964	SK-N-MC	brain:	n/a
27	chr15:77708914-77708964	MCF-7	breast:	n/a
28	chr15:77708914-77708964	NHDF-neo	bronchial:	n/a
29	chr15:77708914-77708964	HRE	kidney:	n/a
30	chr15:77708914-77708964	IMR90	lung:	fetal
31	chr15:77708914-77708964	GM12878	blood:	n/a
32	chr15:77708914-77708964	PANC-1	pancreas:	n/a
33	chr15:77708914-77708964	CMK	blood:	n/a
34	chr15:77708914-77708964	SAEC	small airway:	n/a
35	chr15:77708914-77708964	GM06990	blood:	n/a
36	chr15:77708914-77708964	HRCEpiC	kidney:	n/a
37	chr15:77708914-77708964	Caco-2	colon:	n/a
38	chr15:77708914-77708964	HCT-116	colon:	n/a
39	chr15:77708914-77708964	HAEpiC	amniotic membrane:	n/a
40	chr15:77708914-77708964	T-47D	breast:	n/a
41	chr15:77708914-77708964	BJ	skin:	n/a
42	chr15:77708914-77708964	BE2_C	brain:	n/a
43	chr15:77708914-77708964	U87	brain:	n/a
44	chr15:77708914-77708964	AG04449	skin:	fetal
45	chr15:77708914-77708964	ProgFib	skin:	n/a
46	chr15:77708914-77708964	NB4	blood:	n/a
47	chr15:77708914-77708964	AG04450	lung:	fetal
48	chr15:77708914-77708964	SK-N-SH	brain:	n/a
49	chr15:77708914-77708964	Jurkat	blood:	n/a
50	chr15:77708914-77708964	ECC-1	luminal epithelium:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77686365..77688021-chr15:77708534..77710284,2	K562	blood:
2	chr15:77700084..77701630-chr15:77707595..77709456,2	K562	blood:

No data

Variant related genes	Relation type
HMG20A	TF binding region
HMG20A	CpG island

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10519165	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519166	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898506	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898522	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901298	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905548	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905890	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906093	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906155	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906220	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909547	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909771	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910225	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911362	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12912739	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914885	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917103	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917143	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917211	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917347	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917359	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968817	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968829	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968848	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968851	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384857	0.95[EUR][1000 genomes]
rs17386174	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17469938	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471280	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471809	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17472416	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949269	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036896	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864841	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023254	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34137991	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34158220	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34197100	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34237392	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34344208	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34410684	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34607003	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34660075	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34665451	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34690222	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34772392	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34858590	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34905779	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34918566	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35015654	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35277326	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35347401	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35383172	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35420345	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35450609	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628983	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35775156	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778082	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35834995	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35892909	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36103772	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4288963	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4349115	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007266	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007269	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007278	0.89[ASN][1000 genomes]
rs62007303	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007307	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007310	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007313	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007316	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007337	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007338	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007339	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007340	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62007343	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010561	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010567	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742499	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031202	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907399	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv21291	chr15:77707945-77712363	Active TSS Weak transcription Flanking Active TSS 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34664675	SGK269	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77675000-77709400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:77695600-77709200	Weak transcription	HMEC	breast
3	chr15:77695800-77709400	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:77698600-77711200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:77702200-77709400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:77702600-77711000	Weak transcription	Lung	lung
7	chr15:77702800-77709000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:77702800-77709400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:77702800-77711000	Weak transcription	Aorta	Aorta
10	chr15:77703000-77711400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:77703200-77710800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:77703400-77710000	Weak transcription	Thymus	Thymus
13	chr15:77704400-77709400	Weak transcription	Fetal Intestine Small	intestine
14	chr15:77704400-77709800	Weak transcription	HepG2	liver
15	chr15:77704400-77710000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:77704600-77709400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:77704800-77710800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:77706400-77709800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:77706600-77710400	Weak transcription	Stomach Mucosa	stomach
20	chr15:77707200-77709000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr15:77707200-77709400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:77707200-77709400	Enhancers	Adipose Nuclei	Adipose
23	chr15:77707200-77709600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:77707200-77710600	Enhancers	Fetal Heart	heart
25	chr15:77707200-77710800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr15:77707600-77709600	Enhancers	HUVEC	blood vessel
27	chr15:77707600-77710200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr15:77707600-77710200	Enhancers	Psoas Muscle	Psoas
29	chr15:77707600-77710400	Enhancers	Right Ventricle	heart
30	chr15:77707600-77710600	Enhancers	Ovary	ovary
31	chr15:77707800-77709000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:77707800-77709400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:77707800-77709400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:77707800-77709800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:77707800-77709800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr15:77707800-77710000	Enhancers	Fetal Lung	lung
37	chr15:77707800-77710600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:77707800-77710600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:77707800-77710800	Enhancers	Brain Hippocampus Middle	brain
40	chr15:77707800-77711000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr15:77708000-77709000	Enhancers	Brain Angular Gyrus	brain
42	chr15:77708000-77709000	Enhancers	Dnd41	blood
43	chr15:77708000-77709400	Enhancers	NHDF-Ad	bronchial
44	chr15:77708000-77710000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr15:77708000-77710200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr15:77708000-77710400	Enhancers	Brain Anterior Caudate	brain
47	chr15:77708000-77710600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:77708000-77710600	Enhancers	Fetal Muscle Leg	muscle
49	chr15:77708000-77710800	Weak transcription	Placenta	Placenta
50	chr15:77708200-77709000	Flanking Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links