Variant report

Variant	rs1355438
Chromosome Location	chr3:141767853-141767854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141767270..141770576-chr3:141773885..141776587,3	K562	blood:
2	chr3:141765860..141768702-chr3:141834792..141837643,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10935453	0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11706480	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12496412	0.87[ASN][1000 genomes]
rs13065446	0.85[ASN][1000 genomes]
rs1397764	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1511299	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1543064	0.82[JPT][hapmap]
rs16852073	0.95[YRI][hapmap]
rs16852086	0.86[YRI][hapmap]
rs1704985	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1705607	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1705614	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1705624	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2861422	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2862123	0.81[ASN][1000 genomes]
rs2862124	0.81[ASN][1000 genomes]
rs2862125	0.90[ASN][1000 genomes]
rs34186890	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34392664	0.85[ASN][1000 genomes]
rs347685	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs347686	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs347692	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683658	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57156169	0.82[AFR][1000 genomes]
rs6440057	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6440060	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773343	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6778085	0.82[JPT][hapmap]
rs6781340	0.85[ASN][1000 genomes]
rs6791514	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794342	1.00[ASN][1000 genomes]
rs6795301	0.82[JPT][hapmap]
rs73232681	0.81[ASN][1000 genomes]
rs7630893	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7640665	0.81[EUR][1000 genomes]
rs7644155	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7644383	0.94[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9289641	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9848817	0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs9857917	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9865413	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9865777	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9877536	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9877817	0.92[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9942075	0.88[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS 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	26 gene(s)	inside rSNPs	diseases
5	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv877553	chr3:141732321-141786073	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv877554	chr3:141735532-141781890	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv877555	chr3:141740076-141791408	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	esv2757013	chr3:141756541-142094631	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic 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 miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1355438	CHST2	cis	cerebellum	SCAN
rs1355438	XRN1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141747600-141773000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:141747600-141780400	Weak transcription	Left Ventricle	heart
3	chr3:141753600-141768400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:141755200-141771400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:141758400-141777400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:141758800-141768800	Weak transcription	Esophagus	oesophagus
7	chr3:141758800-141775800	Weak transcription	Ovary	ovary
8	chr3:141760000-141770000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:141760400-141773800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:141760600-141800800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:141760800-141772600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:141760800-141774600	Weak transcription	Liver	Liver
13	chr3:141761000-141772600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:141761000-141773400	Weak transcription	Dnd41	blood
15	chr3:141761000-141781600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:141761000-141807800	Weak transcription	Fetal Lung	lung
17	chr3:141761600-141772200	Weak transcription	Adipose Nuclei	Adipose
18	chr3:141761600-141775600	Weak transcription	NHEK	skin
19	chr3:141761800-141819600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:141762000-141772800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:141762600-141775800	Weak transcription	Lung	lung
22	chr3:141762800-141782800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:141763000-141770000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:141763000-141770000	Weak transcription	Fetal Stomach	stomach
25	chr3:141763000-141771400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:141763000-141772800	Weak transcription	Brain Germinal Matrix	brain
27	chr3:141763000-141775000	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:141763000-141778200	Weak transcription	Fetal Intestine Large	intestine
29	chr3:141763000-141820000	Weak transcription	Pancreas	Pancrea
30	chr3:141763000-141824200	Weak transcription	Aorta	Aorta
31	chr3:141764000-141825600	Weak transcription	Primary T cells from cord blood	blood
32	chr3:141764600-141770000	Weak transcription	Psoas Muscle	Psoas
33	chr3:141765000-141818800	Weak transcription	Primary B cells from cord blood	blood
34	chr3:141766000-141768000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:141766200-141768600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:141766600-141773600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:141767000-141798000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:141767200-141774200	Weak transcription	K562	blood
39	chr3:141767400-141768000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:141767600-141770000	Weak transcription	Thymus	Thymus
41	chr3:141767600-141807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:141767800-141769600	Weak transcription	Fetal Thymus	thymus
43	chr3:141767800-141769800	Weak transcription	Fetal Intestine Small	intestine

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