Variant report

Variant	rs1057713
Chromosome Location	chr9:96714161-96714162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr9:96714099-96714199	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr9:96709708-96717433	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr9:96710652-96717425	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:96713166-96714239	NB4	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:96710015..96712729-chr9:96712737..96714256,2	MCF-7	breast:
2	chr9:96711387..96714258-chr9:96716250..96718266,3	K562	blood:
3	chr9:96706258..96707958-chr9:96711820..96714339,2	MCF-7	breast:
4	chr9:96713619..96716485-chr9:96717370..96719166,2	K562	blood:
5	chr9:96710465..96712948-chr9:96713592..96715312,2	MCF-7	breast:
6	chr9:96709646..96715968-chr9:96715980..96721050,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235601	TF binding region
ENSG00000235601	Chromatin interaction
ENSG00000131668	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10821273	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10821274	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11788035	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11999521	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11999551	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12005806	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1320546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13283836	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13291289	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1933680	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1933681	0.83[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1933682	0.84[AMR][1000 genomes]
rs2095778	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35001304	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4437716	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4563951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56285369	0.80[AMR][1000 genomes]
rs7034685	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7872123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1057713	IPPK	cis	parietal	SCAN
rs1057713	ORMDL2	trans	parietal	SCAN
rs1057713	SPTLC1	cis	cerebellum	SCAN
rs1057713	WNK2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96711600-96715600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
2	chr9:96712800-96714800	Bivalent/Poised TSS	HSMM	muscle
3	chr9:96713000-96714200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
4	chr9:96713000-96714400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
5	chr9:96713000-96714400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
6	chr9:96713000-96714600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
7	chr9:96713000-96714800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:96713000-96715800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr9:96713000-96717000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
10	chr9:96713200-96714200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr9:96713200-96714200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:96713200-96714200	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
13	chr9:96713200-96714200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
14	chr9:96713200-96714200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
15	chr9:96713200-96714200	Bivalent/Poised TSS	NHEK	skin
16	chr9:96713200-96714400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
17	chr9:96713200-96714600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:96713200-96714600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:96713200-96715000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:96713200-96715000	Bivalent Enhancer	Fetal Heart	heart
21	chr9:96713200-96716400	Bivalent Enhancer	Fetal Brain Male	brain
22	chr9:96713400-96714200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr9:96713400-96714200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:96713400-96714200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr9:96713400-96714200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
26	chr9:96713400-96714600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:96713400-96714800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
28	chr9:96713600-96714200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
29	chr9:96713600-96714600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
30	chr9:96713600-96716400	Weak transcription	Hela-S3	cervix
31	chr9:96713800-96714200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr9:96713800-96714200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr9:96713800-96714200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:96713800-96714200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
35	chr9:96713800-96714200	Active TSS	Aorta	Aorta
36	chr9:96713800-96714200	Bivalent Enhancer	Brain Angular Gyrus	brain
37	chr9:96713800-96714200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
38	chr9:96713800-96714200	Bivalent Enhancer	Small Intestine	intestine
39	chr9:96713800-96714400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:96713800-96714400	Bivalent Enhancer	Primary B cells from cord blood	blood
41	chr9:96713800-96714400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr9:96713800-96714400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:96713800-96714600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
44	chr9:96713800-96714600	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr9:96713800-96715000	Bivalent Enhancer	Fetal Intestine Small	intestine
46	chr9:96713800-96715200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:96713800-96715200	Bivalent Enhancer	Fetal Intestine Large	intestine
48	chr9:96713800-96715200	Bivalent Enhancer	Placenta	Placenta
49	chr9:96713800-96715800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:96713800-96715800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links