Variant report

Variant	rs4627
Chromosome Location	chr3:142526594-142526595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142524560..142526927-chr3:142527541..142530171,3	K562	blood:
2	chr3:142526371..142529664-chr3:142531134..142533602,3	K562	blood:
3	chr3:142519586..142522583-chr3:142524020..142526626,3	K562	blood:
4	chr3:142517462..142521813-chr3:142523317..142528126,6	K562	blood:
5	chr3:142517462..142519257-chr3:142525193..142528126,2	K562	blood:
6	chr3:142526371..142529815-chr3:142530861..142533602,4	K562	blood:

Variant related genes	Relation type
ENSG00000251787	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11716882	1.00[CEU][hapmap]
rs13086677	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16852464	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs16852543	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap]
rs2354859	1.00[CEU][hapmap]
rs9845606	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000631	chr3:142516367-142572058	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4627	XRN1	cis	cerebellum	SCAN
rs4627	TRPC1	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142468400-142526800	Weak transcription	NHDF-Ad	bronchial
2	chr3:142468400-142529400	Weak transcription	Brain Germinal Matrix	brain
3	chr3:142475000-142527200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:142488800-142527000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:142490200-142529400	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:142495400-142527000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:142498600-142526800	Weak transcription	Osteobl	bone
8	chr3:142499000-142527000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:142499400-142547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:142501800-142527000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:142501800-142528000	Weak transcription	Left Ventricle	heart
12	chr3:142501800-142535600	Weak transcription	Aorta	Aorta
13	chr3:142502000-142529400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:142510400-142527200	Weak transcription	A549	lung
15	chr3:142513600-142527200	Weak transcription	Brain Substantia Nigra	brain
16	chr3:142514800-142572000	Weak transcription	Right Ventricle	heart
17	chr3:142515000-142530800	Weak transcription	HSMM	muscle
18	chr3:142515600-142527000	Weak transcription	K562	blood
19	chr3:142517600-142526800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:142518800-142527200	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:142519000-142572000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:142519200-142526600	Weak transcription	NHLF	lung
23	chr3:142519800-142530000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:142521400-142528800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:142521600-142526800	Weak transcription	NH-A	brain
26	chr3:142522200-142526600	Weak transcription	Fetal Lung	lung
27	chr3:142522200-142526800	Weak transcription	HMEC	breast
28	chr3:142522200-142551800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:142522400-142530000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:142522800-142528600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:142523000-142528200	Weak transcription	Ovary	ovary
32	chr3:142523600-142526800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:142523600-142526800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:142523800-142527200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:142523800-142539400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:142524000-142526800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:142524000-142527000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:142524000-142528600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:142524000-142530600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:142524000-142531400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:142524800-142561000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:142525000-142526600	Weak transcription	Adipose Nuclei	Adipose
43	chr3:142525000-142526800	Weak transcription	Fetal Heart	heart
44	chr3:142525000-142538600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:142525000-142543800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:142525000-142555800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:142525200-142526800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:142525200-142527000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:142525200-142527200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:142525200-142539000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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