Variant report

Variant	rs4846228
Chromosome Location	chr1:10552718-10552719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10489277..10492525-chr1:10551215..10553399,3	MCF-7	breast:
2	chr1:10532825..10535094-chr1:10550746..10552917,2	K562	blood:
3	chr1:10549510..10553180-chr1:10560957..10564182,4	K562	blood:
4	chr1:10552588..10555183-chr1:10557797..10560030,2	MCF-7	breast:
5	chr1:10549897..10551721-chr1:10551750..10553433,2	K562	blood:
6	chr1:10534413..10537768-chr1:10551238..10554957,5	K562	blood:

Variant related genes	Relation type
ENSG00000251503	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000271989	Chromatin interaction
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17035156	0.84[TSI][hapmap]
rs2480786	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs2480787	0.80[EUR][1000 genomes]
rs2483678	0.84[TSI][hapmap]
rs2506878	0.85[TSI][hapmap]
rs2506887	0.84[TSI][hapmap]
rs2988399	0.88[EUR][1000 genomes]
rs3828044	1.00[CHB][hapmap]
rs9970001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4846228	PEX14	cis	multi-tissue	Pritchard
rs4846228	APITD1	cis	cerebellum	SCAN
rs4846228	KIF1B	Cis_1M	lymphoblastoid	RTeQTL
rs4846228	FBXO44	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10535800-10555000	Weak transcription	Aorta	Aorta
2	chr1:10536000-10555000	Weak transcription	Esophagus	oesophagus
3	chr1:10536000-10555000	Weak transcription	HSMMtube	muscle
4	chr1:10536000-10555600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:10536200-10555000	Weak transcription	NH-A	brain
6	chr1:10536400-10553000	Weak transcription	Psoas Muscle	Psoas
7	chr1:10536400-10554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:10536400-10554600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:10536400-10554800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:10536400-10554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:10536400-10554800	Weak transcription	Fetal Brain Male	brain
12	chr1:10536400-10554800	Weak transcription	NHDF-Ad	bronchial
13	chr1:10536400-10555000	Weak transcription	Fetal Kidney	kidney
14	chr1:10536400-10555000	Weak transcription	HSMM	muscle
15	chr1:10536600-10554800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:10536600-10555000	Weak transcription	Brain Substantia Nigra	brain
17	chr1:10536800-10554600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:10536800-10554600	Weak transcription	Pancreas	Pancrea
19	chr1:10536800-10554600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:10537000-10554600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:10537000-10554800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:10537000-10554800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:10537600-10554800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:10537800-10554400	Weak transcription	Dnd41	blood
25	chr1:10540600-10555600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:10545200-10554600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:10545200-10554600	Weak transcription	Osteobl	bone
28	chr1:10545200-10554800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:10545400-10554800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:10549800-10554600	Weak transcription	Hela-S3	cervix
31	chr1:10550000-10554400	Weak transcription	GM12878-XiMat	blood
32	chr1:10550000-10554600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:10550000-10554600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:10550000-10554800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:10550000-10554800	Weak transcription	Colonic Mucosa	Colon
36	chr1:10550000-10554800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:10550000-10555000	Weak transcription	A549	lung
38	chr1:10550200-10554600	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:10550200-10554600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:10550200-10554600	Weak transcription	Fetal Thymus	thymus
41	chr1:10550200-10554600	Weak transcription	Stomach Mucosa	stomach
42	chr1:10550200-10554800	Weak transcription	Fetal Lung	lung
43	chr1:10550200-10555000	Weak transcription	Small Intestine	intestine
44	chr1:10550400-10553600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:10550400-10553800	Weak transcription	Adipose Nuclei	Adipose
46	chr1:10550400-10554000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:10550400-10554200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:10550400-10554200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:10550400-10554400	Weak transcription	K562	blood
50	chr1:10550400-10554600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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