Variant report

Variant	rs9942
Chromosome Location	chr3:141663752-141663753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141662334..141665277-chr3:141666881..141671768,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFDP2-5	chr3:141663270-141666233	ENSG00000269905.1

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1045279	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804681	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11569216	0.85[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11569256	0.81[EUR][1000 genomes]
rs12495978	0.85[CEU][hapmap]
rs1976633	0.85[ASN][1000 genomes]
rs2861421	0.81[EUR][1000 genomes]
rs34773643	0.87[EUR][1000 genomes]
rs3811708	0.85[CEU][hapmap]
rs4234470	0.85[JPT][hapmap]
rs6440053	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440054	0.87[EUR][1000 genomes]
rs6788524	1.00[YRI][hapmap]
rs7617280	1.00[YRI][hapmap]
rs7652258	0.88[YRI][hapmap]
rs9815587	0.87[EUR][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	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	esv3355546	chr3:141660462-141664660	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9942	XRN1	cis	parietal	SCAN
rs9942	ZIC4	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
2	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
6	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
8	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:141643000-141675800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:141643400-141671200	Weak transcription	Right Ventricle	heart
11	chr3:141644800-141678400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:141646800-141668200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:141647000-141668400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:141647000-141669200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:141647200-141669400	Weak transcription	Primary B cells from cord blood	blood
16	chr3:141647400-141668200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:141647400-141670400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:141647600-141670600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:141647800-141664200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:141647800-141668200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:141647800-141670200	Weak transcription	Adipose Nuclei	Adipose
22	chr3:141648000-141664400	Weak transcription	Primary T cells from cord blood	blood
23	chr3:141648000-141670000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:141648000-141670800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:141650000-141664200	Weak transcription	Dnd41	blood
26	chr3:141653200-141664400	Weak transcription	Fetal Stomach	stomach
27	chr3:141653400-141664200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:141656600-141664400	Weak transcription	Esophagus	oesophagus
29	chr3:141656800-141664200	Weak transcription	Thymus	Thymus
30	chr3:141657000-141664600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:141659200-141696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:141659400-141664000	Weak transcription	Fetal Thymus	thymus
33	chr3:141659400-141664400	Weak transcription	HSMMtube	muscle
34	chr3:141659400-141668400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:141659400-141673800	Weak transcription	Brain Germinal Matrix	brain
36	chr3:141659400-141678400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:141659600-141664400	Weak transcription	HSMM	muscle
38	chr3:141659600-141664600	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr3:141659600-141669400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:141659600-141670400	Weak transcription	NH-A	brain
41	chr3:141659600-141670800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:141659600-141671200	Weak transcription	Pancreas	Pancrea
43	chr3:141659600-141671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:141659600-141674000	Weak transcription	NHLF	lung
45	chr3:141659600-141676000	Weak transcription	Fetal Heart	heart
46	chr3:141659600-141676400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:141659600-141678200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:141659600-141678200	Weak transcription	NHDF-Ad	bronchial
49	chr3:141659600-141678400	Weak transcription	A549	lung
50	chr3:141660000-141664400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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