Variant report

Variant	rs1107675
Chromosome Location	chr4:57838707-57838708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
2	chr4:57832993..57836325-chr4:57837117..57839570,3	K562	blood:
3	chr4:57832384..57834493-chr4:57837035..57839570,2	K562	blood:

Variant related genes	Relation type
ENSG00000269949	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10018580	0.84[CEU][hapmap]
rs10866440	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10866441	0.94[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1105434	0.94[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap]
rs11727683	0.82[ASN][1000 genomes]
rs11729152	0.90[ASN][1000 genomes]
rs11730321	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11736192	0.82[ASN][1000 genomes]
rs11736808	0.86[ASN][1000 genomes]
rs11736869	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs11737689	0.82[ASN][1000 genomes]
rs11930475	0.84[CEU][hapmap]
rs11932673	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500454	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12501224	0.83[ASN][1000 genomes]
rs12502076	0.82[ASN][1000 genomes]
rs1277271	0.93[ASN][1000 genomes]
rs1277287	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1277288	0.83[ASN][1000 genomes]
rs13108245	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs13121176	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13131605	0.81[ASN][1000 genomes]
rs13133792	0.84[CEU][hapmap]
rs13136432	0.83[ASN][1000 genomes]
rs1315005	0.83[ASN][1000 genomes]
rs13150593	0.83[ASN][1000 genomes]
rs1625691	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17081937	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17087307	0.99[ASN][1000 genomes]
rs17087317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17087332	0.83[CEU][hapmap]
rs17087382	0.84[CEU][hapmap]
rs17087411	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs17087414	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1718839	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1877669	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1976780	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2014870	0.81[ASN][1000 genomes]
rs2228991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3000	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs34124552	0.83[ASN][1000 genomes]
rs34448457	0.83[ASN][1000 genomes]
rs34576794	0.92[ASN][1000 genomes]
rs34659774	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35267092	0.83[ASN][1000 genomes]
rs3733306	0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs3796528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3806745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41552420	0.80[ASN][1000 genomes]
rs41556916	0.82[ASN][1000 genomes]
rs56182208	0.82[ASN][1000 genomes]
rs56285301	0.82[ASN][1000 genomes]
rs57469512	0.82[ASN][1000 genomes]
rs62308155	0.82[ASN][1000 genomes]
rs6554398	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6554399	0.89[ASN][1000 genomes]
rs6816457	0.93[ASN][1000 genomes]
rs6838948	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6847086	0.82[JPT][hapmap]
rs6852110	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs73242616	0.88[ASN][1000 genomes]
rs73242631	0.80[ASN][1000 genomes]
rs7440152	0.84[CEU][hapmap]
rs7661194	1.00[JPT][hapmap]
rs7680734	0.94[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap]
rs7685576	0.88[ASN][1000 genomes]
rs781665	0.93[ASN][1000 genomes]
rs781666	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs781668	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9942208	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996331	0.83[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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh 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	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1107675	SPINK2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57793600-57842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:57793600-57842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57826400-57839800	Strong transcription	Primary T cells from cord blood	blood
4	chr4:57826600-57838800	Strong transcription	Liver	Liver
5	chr4:57826600-57839000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:57826600-57839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:57826600-57840800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:57826600-57840800	Strong transcription	Fetal Brain Female	brain
9	chr4:57826600-57840800	Strong transcription	Fetal Muscle Leg	muscle
10	chr4:57826600-57840800	Strong transcription	Fetal Thymus	thymus
11	chr4:57826600-57841000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:57826600-57841400	Strong transcription	Fetal Intestine Large	intestine
13	chr4:57826800-57839000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:57826800-57840800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:57826800-57840800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:57826800-57840800	Weak transcription	Stomach Mucosa	stomach
17	chr4:57827000-57840400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:57827000-57843200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:57827200-57838800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:57827200-57839000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:57827200-57840200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr4:57827200-57840400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:57827200-57840400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:57827200-57840600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:57827200-57840800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:57827200-57840800	Strong transcription	Dnd41	blood
27	chr4:57827200-57841000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:57827200-57841000	Strong transcription	Fetal Lung	lung
29	chr4:57827200-57841400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:57827400-57838800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:57827400-57838800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:57827400-57839600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr4:57827400-57839600	Strong transcription	Placenta	Placenta
34	chr4:57827400-57841000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:57827600-57840200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:57827600-57840600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:57827800-57839200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:57827800-57839200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:57828000-57840400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr4:57828000-57840600	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:57828200-57838800	Strong transcription	Adipose Nuclei	Adipose
42	chr4:57828200-57838800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:57828200-57838800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:57828200-57840200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:57828200-57840400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:57828200-57841200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:57828400-57838800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr4:57828400-57839000	Strong transcription	Brain Germinal Matrix	brain
49	chr4:57828400-57839200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr4:57828400-57839200	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links