Variant report

Variant	rs11932673
Chromosome Location	chr4:57833203-57833204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57832993..57836325-chr4:57837117..57839570,3	K562	blood:
2	chr4:57832384..57834493-chr4:57837035..57839570,2	K562	blood:
3	chr4:57831762..57836604-chr4:57841016..57847876,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000084092	Chromatin interaction
ENSG00000047315	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	0.88[TSI][hapmap]
rs10866440	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10866441	0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1105434	0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1107675	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]
rs11727683	0.81[ASN][1000 genomes]
rs11729152	0.91[ASN][1000 genomes]
rs11730321	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11736192	0.83[ASN][1000 genomes]
rs11736808	0.87[ASN][1000 genomes]
rs11736869	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs11737689	0.82[ASN][1000 genomes]
rs11930475	0.88[TSI][hapmap]
rs12500454	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12501224	0.84[ASN][1000 genomes]
rs12501990	0.80[ASN][1000 genomes]
rs12502076	0.83[ASN][1000 genomes]
rs1277271	0.92[ASN][1000 genomes]
rs1277287	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1277288	0.82[ASN][1000 genomes]
rs13108245	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs13121176	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13131605	0.82[ASN][1000 genomes]
rs13133792	0.88[TSI][hapmap]
rs13136432	0.84[ASN][1000 genomes]
rs1315005	0.82[ASN][1000 genomes]
rs13150593	0.84[ASN][1000 genomes]
rs1625691	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17081937	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17087307	1.00[ASN][1000 genomes]
rs17087317	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17087332	0.87[GIH][hapmap];0.88[TSI][hapmap]
rs17087411	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs17087414	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs17181222	0.88[TSI][hapmap]
rs1718839	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1877669	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1976780	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014870	0.82[ASN][1000 genomes]
rs2228991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3000	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs34124552	0.84[ASN][1000 genomes]
rs34448457	0.84[ASN][1000 genomes]
rs34576794	0.91[ASN][1000 genomes]
rs34659774	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35267092	0.84[ASN][1000 genomes]
rs3733306	0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs3796528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3806745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs41556916	0.81[ASN][1000 genomes]
rs4864608	0.80[ASN][1000 genomes]
rs56182208	0.81[ASN][1000 genomes]
rs56285301	0.81[ASN][1000 genomes]
rs57469512	0.81[ASN][1000 genomes]
rs62308155	0.83[ASN][1000 genomes]
rs6554398	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6554399	0.90[ASN][1000 genomes]
rs6816457	0.92[ASN][1000 genomes]
rs6838948	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6847086	0.82[JPT][hapmap]
rs6852110	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs73242616	0.88[ASN][1000 genomes]
rs7440152	0.88[TSI][hapmap]
rs7661194	1.00[JPT][hapmap]
rs7680734	0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7685576	0.88[ASN][1000 genomes]
rs781665	0.93[ASN][1000 genomes]
rs781666	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs781668	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9942208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996331	0.84[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
rs11932673	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	chr4:57820200-57836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:57820200-57836000	Weak transcription	Esophagus	oesophagus
5	chr4:57824600-57838400	Weak transcription	Aorta	Aorta
6	chr4:57825600-57838600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:57826400-57839800	Strong transcription	Primary T cells from cord blood	blood
8	chr4:57826600-57833400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:57826600-57834400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr4:57826600-57834600	Strong transcription	Fetal Stomach	stomach
11	chr4:57826600-57835200	Strong transcription	Brain Anterior Caudate	brain
12	chr4:57826600-57838600	Strong transcription	Fetal Intestine Small	intestine
13	chr4:57826600-57838800	Strong transcription	Liver	Liver
14	chr4:57826600-57839000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:57826600-57839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:57826600-57840800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:57826600-57840800	Strong transcription	Fetal Brain Female	brain
18	chr4:57826600-57840800	Strong transcription	Fetal Muscle Leg	muscle
19	chr4:57826600-57840800	Strong transcription	Fetal Thymus	thymus
20	chr4:57826600-57841000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:57826600-57841400	Strong transcription	Fetal Intestine Large	intestine
22	chr4:57826800-57839000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:57826800-57840800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:57826800-57840800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:57826800-57840800	Weak transcription	Stomach Mucosa	stomach
26	chr4:57827000-57838400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:57827000-57840400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:57827000-57843200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr4:57827200-57833600	Strong transcription	Thymus	Thymus
30	chr4:57827200-57835200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr4:57827200-57835400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:57827200-57838400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:57827200-57838800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:57827200-57839000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:57827200-57840200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr4:57827200-57840400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:57827200-57840400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:57827200-57840600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:57827200-57840800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:57827200-57840800	Strong transcription	Dnd41	blood
41	chr4:57827200-57841000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:57827200-57841000	Strong transcription	Fetal Lung	lung
43	chr4:57827200-57841400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:57827400-57833600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr4:57827400-57838400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:57827400-57838800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:57827400-57838800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:57827400-57839600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr4:57827400-57839600	Strong transcription	Placenta	Placenta
50	chr4:57827400-57841000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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