Variant report

Variant	rs6440052
Chromosome Location	chr3:141659241-141659242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141456126..141457791-chr3:141659173..141662093,2	MCF-7	breast:
2	chr3:141658582..141660731-chr3:141665381..141667726,2	K562	blood:
3	chr3:141629759..141632331-chr3:141657895..141659555,2	K562	blood:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction
ENSG00000269905	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1131029	0.88[CEU][hapmap]
rs12636926	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637444	0.83[ASN][1000 genomes]
rs13077550	0.82[EUR][1000 genomes]
rs3762727	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792409	0.88[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683653	0.89[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs6765439	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628851	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7642874	0.94[CHD][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs9289639	0.81[EUR][1000 genomes]
rs9817526	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9861009	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6440052	RBP2	cis	parietal	SCAN
rs6440052	XRN1	cis	parietal	SCAN

Chromatin state (count:90 , 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	chr3:141647800-141660800	Weak transcription	Lung	lung
20	chr3:141647800-141664200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:141647800-141668200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:141647800-141670200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:141648000-141660600	Weak transcription	Gastric	stomach
24	chr3:141648000-141664400	Weak transcription	Primary T cells from cord blood	blood
25	chr3:141648000-141670000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:141648000-141670800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:141648200-141663400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:141648600-141660200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:141650000-141664200	Weak transcription	Dnd41	blood
30	chr3:141653200-141664400	Weak transcription	Fetal Stomach	stomach
31	chr3:141653400-141664200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:141656400-141660200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:141656400-141660600	Enhancers	Fetal Brain Male	brain
34	chr3:141656600-141664400	Weak transcription	Esophagus	oesophagus
35	chr3:141656800-141660600	Weak transcription	K562	blood
36	chr3:141656800-141664200	Weak transcription	Thymus	Thymus
37	chr3:141657000-141660800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:141657000-141664600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:141657200-141659400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:141657200-141659600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:141658000-141661400	Enhancers	Fetal Intestine Large	intestine
42	chr3:141658600-141659400	Strong transcription	Fetal Thymus	thymus
43	chr3:141658600-141659600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:141658600-141659600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:141658600-141659600	Enhancers	A549	lung
46	chr3:141658600-141659600	Enhancers	NHDF-Ad	bronchial
47	chr3:141658600-141659800	Enhancers	Osteobl	bone
48	chr3:141658600-141660000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr3:141658600-141660000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:141658600-141660000	Enhancers	Fetal Muscle Leg	muscle

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