Variant report

Variant	rs16970325
Chromosome Location	chr15:40373131-40373132
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	TEAD4	chr15:40372751-40373486	K562	blood:	n/a	n/a
2	GATA1	chr15:40372514-40374402	K562	blood:	n/a	chr15:40373145-40373166 chr15:40372880-40372889 chr15:40373220-40373229 chr15:40372927-40372934
3	MYC	chr15:40372818-40374377	K562	blood:	n/a	n/a
4	EP300	chr15:40372946-40373482	K562	blood:	n/a	n/a
5	MAZ	chr15:40372951-40373389	K562	blood:	n/a	n/a
6	RCOR1	chr15:40372868-40373479	K562	blood:	n/a	n/a
7	MAX	chr15:40372987-40373343	K562	blood:	n/a	n/a
8	POLR2A	chr15:40372535-40375358	HepG2	liver:	n/a	n/a
9	RCOR1	chr15:40373040-40373350	K562	blood:	n/a	n/a
10	UBTF	chr15:40373035-40373316	K562	blood:	n/a	n/a
11	POLR2A	chr15:40372428-40373324	HepG2	liver:	n/a	n/a
12	GATA2	chr15:40372915-40373547	HUVEC	blood vessel:	n/a	chr15:40373145-40373166 chr15:40373220-40373229 chr15:40372927-40372934
13	POLR2A	chr15:40372779-40375112	HUVEC	blood vessel:	n/a	n/a
14	ZMIZ1	chr15:40372842-40373365	K562	blood:	n/a	n/a
15	CCNT2	chr15:40372963-40373354	K562	blood:	n/a	n/a
16	GATA3	chr15:40372954-40373335	T-47D	breast:	n/a	chr15:40373145-40373166 chr15:40373220-40373229
17	GATA1	chr15:40372553-40373997	PBDE	blood:	n/a	chr15:40373145-40373166 chr15:40372880-40372889 chr15:40373220-40373229 chr15:40372927-40372934
18	TAL1	chr15:40372807-40373446	K562	blood:	n/a	chr15:40373244-40373262 chr15:40373219-40373227
19	KAP1	chr15:40372863-40373347	U2OS	brain:	n/a	n/a
20	GATA3	chr15:40372972-40373351	T-47D	breast:	n/a	chr15:40373145-40373166 chr15:40373220-40373229
21	GATA2	chr15:40372940-40373394	K562	blood:	n/a	chr15:40373145-40373166 chr15:40373220-40373229
22	MYC	chr15:40372855-40373447	K562	blood:	n/a	n/a
23	USF1	chr15:40373000-40373360	K562	blood:	n/a	n/a
24	BHLHE40	chr15:40372598-40373434	K562	blood:	n/a	n/a
25	SIRT6	chr15:40372900-40373581	K562	blood:	n/a	n/a
26	CUX1	chr15:40372914-40373458	K562	blood:	n/a	n/a
27	POLR2A	chr15:40372860-40373562	HUVEC	blood vessel:	n/a	n/a
28	MAFK	chr15:40372943-40373300	K562	blood:	n/a	n/a
29	ARID3A	chr15:40372900-40373342	K562	blood:	n/a	n/a
30	TBL1XR1	chr15:40373003-40373440	K562	blood:	n/a	n/a
31	USF1	chr15:40373067-40373244	K562	blood:	n/a	n/a
32	TEAD4	chr15:40372976-40373415	K562	blood:	n/a	n/a
33	JUND	chr15:40372709-40373558	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40358638..40360485-chr15:40371045..40374083,3	K562	blood:
2	chr15:40371048..40373362-chr15:40379784..40381665,2	MCF-7	breast:
3	chr15:40358140..40360248-chr15:40371416..40374083,2	K562	blood:
4	chr15:40372039..40375867-chr15:40386826..40392262,4	K562	blood:
5	chr15:40372710..40375354-chr15:40380441..40382230,2	K562	blood:
6	chr15:40371657..40374195-chr15:40453312..40456256,2	K562	blood:
7	chr15:40372535..40375363-chr15:40378032..40381941,5	K562	blood:
8	chr15:40371046..40373186-chr15:40375916..40377601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259584	TF binding region
ENSG00000259409	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16970305	0.92[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs16970319	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17723133	0.85[JPT][hapmap]
rs3803361	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16970325	CRABP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40362200-40373600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:40362400-40374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:40362600-40373800	Weak transcription	Aorta	Aorta
4	chr15:40364800-40376800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:40365000-40373200	Weak transcription	Left Ventricle	heart
6	chr15:40365600-40374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:40368000-40373400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:40368200-40373800	Weak transcription	Pancreas	Pancrea
9	chr15:40368200-40374000	Weak transcription	Gastric	stomach
10	chr15:40368600-40374000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:40369400-40373600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:40369600-40373800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:40372400-40373200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:40372400-40373200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:40372400-40373200	Enhancers	Colon Smooth Muscle	Colon
16	chr15:40372400-40373600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:40372400-40373600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:40372400-40373600	Enhancers	NHLF	lung
19	chr15:40372400-40373800	Enhancers	Primary B cells from peripheral blood	blood
20	chr15:40372400-40373800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:40372400-40373800	Enhancers	Fetal Intestine Large	intestine
22	chr15:40372400-40376400	Enhancers	Fetal Heart	heart
23	chr15:40372600-40373200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:40372600-40373200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:40372600-40373400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr15:40372600-40373600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:40372600-40373600	Enhancers	Brain Substantia Nigra	brain
28	chr15:40372600-40373600	Enhancers	Fetal Intestine Small	intestine
29	chr15:40372600-40373600	Enhancers	Psoas Muscle	Psoas
30	chr15:40372600-40373600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr15:40372600-40373600	Enhancers	Small Intestine	intestine
32	chr15:40372600-40373800	Enhancers	Brain Anterior Caudate	brain
33	chr15:40372600-40373800	Enhancers	Fetal Lung	lung
34	chr15:40372600-40373800	Enhancers	Rectal Smooth Muscle	rectum
35	chr15:40372800-40373200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:40372800-40373400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
37	chr15:40372800-40373400	Flanking Active TSS	HepG2	liver
38	chr15:40372800-40373600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
39	chr15:40372800-40373600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
40	chr15:40372800-40373600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:40372800-40373600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:40372800-40373600	Enhancers	Liver	Liver
43	chr15:40372800-40373600	Enhancers	Colonic Mucosa	Colon
44	chr15:40372800-40373600	Enhancers	Duodenum Mucosa	Duodenum
45	chr15:40372800-40373600	Enhancers	Fetal Thymus	thymus
46	chr15:40372800-40373800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
47	chr15:40372800-40373800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr15:40372800-40373800	Enhancers	Fetal Kidney	kidney
49	chr15:40372800-40373800	Enhancers	A549	lung
50	chr15:40372800-40373800	Enhancers	NH-A	brain

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