Variant report

Variant	rs4839000
Chromosome Location	chr1:114280135-114280136
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114279918..114281737-chr1:114354339..114355849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081019	Chromatin interaction
ENSG00000231128	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11582409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11584821	0.81[JPT][hapmap]
rs17031795	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17274627	0.92[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17359281	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs17359378	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17359468	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17461918	0.86[CEU][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap]
rs17463292	0.91[ASN][1000 genomes]
rs17508449	0.86[CEU][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap]
rs17509844	0.89[ASN][1000 genomes]
rs17510162	0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2146018	0.82[EUR][1000 genomes]
rs3195954	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[ASN][1000 genomes]
rs34122108	0.89[ASN][1000 genomes]
rs35173468	0.89[ASN][1000 genomes]
rs3761934	0.82[EUR][1000 genomes]
rs3761935	0.91[ASN][1000 genomes]
rs3765598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3789604	0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs3789608	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs3811021	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3827733	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs41352847	0.82[EUR][1000 genomes]
rs4393155	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4589108	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4838993	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4838994	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4839331	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4839333	0.85[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs4839336	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4839341	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4839346	0.89[ASN][1000 genomes]
rs55646484	0.89[ASN][1000 genomes]
rs55940960	0.91[ASN][1000 genomes]
rs55951516	0.91[ASN][1000 genomes]
rs6658523	0.89[ASN][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	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers 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	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4839000	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs4839000	PHTF1	cis	lymphoblastoid	seeQTL
rs4839000	KCNA10	cis	parietal	SCAN
rs4839000	CD53	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
2	chr1:114228000-114287800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:114236400-114300000	Weak transcription	Small Intestine	intestine
4	chr1:114242000-114300000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:114245600-114300600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:114248800-114290200	Weak transcription	HMEC	breast
7	chr1:114251000-114291400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:114256600-114283600	Weak transcription	Brain Anterior Caudate	brain
9	chr1:114256600-114288800	Weak transcription	K562	blood
10	chr1:114257600-114283000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:114257600-114296200	Weak transcription	Pancreas	Pancrea
12	chr1:114258000-114300000	Weak transcription	Right Ventricle	heart
13	chr1:114261400-114300000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:114261400-114300600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:114261400-114301000	Weak transcription	Lung	lung
16	chr1:114261600-114280200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:114261600-114300200	Weak transcription	Brain Angular Gyrus	brain
18	chr1:114261600-114300600	Weak transcription	Aorta	Aorta
19	chr1:114261600-114300600	Weak transcription	Esophagus	oesophagus
20	chr1:114261600-114300600	Weak transcription	Gastric	stomach
21	chr1:114262000-114286400	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:114263600-114285400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:114263600-114300000	Weak transcription	Fetal Lung	lung
24	chr1:114263600-114300400	Weak transcription	Fetal Intestine Large	intestine
25	chr1:114264000-114300400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:114264200-114300000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:114264400-114288200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:114264800-114290200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:114265000-114283600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:114265000-114291200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:114265200-114283600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:114265600-114281000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:114267200-114290000	Weak transcription	NHEK	skin
34	chr1:114267400-114299400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:114267400-114300000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:114268400-114292000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:114268400-114298000	Weak transcription	A549	lung
38	chr1:114268600-114292000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:114268600-114292600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:114268600-114296200	Weak transcription	Fetal Intestine Small	intestine
41	chr1:114268800-114296400	Weak transcription	NHLF	lung
42	chr1:114268800-114299200	Weak transcription	Fetal Brain Female	brain
43	chr1:114269200-114296000	Weak transcription	Ovary	ovary
44	chr1:114271000-114287400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:114271200-114283000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:114272200-114281400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:114272200-114281400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:114272800-114300000	Weak transcription	Primary B cells from cord blood	blood
49	chr1:114274200-114281600	Weak transcription	Primary T cells from cord blood	blood
50	chr1:114274600-114281200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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