Variant report

Variant	rs4899241
Chromosome Location	chr14:68864311-68864312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:68863962..68866276-chr14:68924626..68928147,6	MCF-7	breast:
2	chr14:68863838..68866613-chr14:68869983..68873336,6	MCF-7	breast:
3	chr14:68862313..68866033-chr14:69260307..69264039,7	MCF-7	breast:
4	chr14:68605654..68608460-chr14:68861850..68864803,2	MCF-7	breast:
5	chr14:68859762..68864000-chr14:68864300..68866609,3	K562	blood:
6	chr14:68858725..68872867-chr14:69250734..69263104,36	MCF-7	breast:
7	chr14:68749573..68752589-chr14:68864032..68866537,3	MCF-7	breast:
8	chr14:68862930..68865913-chr14:68933149..68936719,4	MCF-7	breast:
9	chr14:68862987..68864595-chr14:68942546..68944061,2	MCF-7	breast:
10	chr14:68863198..68864811-chr14:68906969..68909048,2	MCF-7	breast:
11	chr14:68864311..68866713-chr14:68933323..68935955,2	MCF-7	breast:
12	chr14:68863146..68866898-chr14:68882756..68885018,4	MCF-7	breast:
13	chr14:68825944..68827460-chr14:68863306..68865139,2	MCF-7	breast:
14	chr14:68862766..68869873-chr14:69251663..69259874,10	MCF-7	breast:
15	chr14:68829073..68831953-chr14:68862651..68864586,2	MCF-7	breast:
16	chr14:68857574..68861262-chr14:68863734..68866586,4	K562	blood:
17	chr14:68863006..68865932-chr14:69077018..69079780,3	MCF-7	breast:
18	chr14:68863291..68866067-chr14:68920468..68924017,3	MCF-7	breast:
19	chr14:68773029..68777937-chr14:68858584..68866534,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10747299	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11158737	1.00[JPT][hapmap]
rs11158742	1.00[JPT][hapmap]
rs12435006	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12588330	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12897307	1.00[JPT][hapmap]
rs17755674	1.00[JPT][hapmap]
rs1956538	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2064910	1.00[JPT][hapmap]
rs2331703	0.85[CHD][hapmap];0.88[GIH][hapmap]
rs2331704	0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2525507	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2753403	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2842320	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3784118	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3966077	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4899243	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4902578	1.00[JPT][hapmap]
rs4902580	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4902581	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4902587	1.00[JPT][hapmap]
rs4902588	1.00[JPT][hapmap]
rs4902589	1.00[JPT][hapmap]
rs7145422	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7152152	0.85[GIH][hapmap]
rs7154175	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8003606	1.00[CHB][hapmap]
rs8013184	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8019592	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323510	1.00[JPT][hapmap]
rs975422	1.00[JPT][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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4899241	EIF2S1	cis	cerebellum	SCAN
rs4899241	MED6	cis	cerebellum	SCAN
rs4899241	UPF0639	cis	cerebellum	SCAN
rs4899241	MAP3K9	cis	parietal	SCAN
rs4899241	CHURC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68856600-68865400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:68857000-68865800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr14:68858000-68865200	Enhancers	NHLF	lung
4	chr14:68858000-68865800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr14:68858200-68865600	Enhancers	Placenta	Placenta
6	chr14:68858400-68865200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr14:68858800-68865600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:68859000-68865400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:68859000-68865800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr14:68859200-68865200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr14:68859600-68864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:68859800-68871400	Weak transcription	Gastric	stomach
13	chr14:68860600-68864600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:68860600-68865600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr14:68860800-68865000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr14:68860800-68865400	Enhancers	NHDF-Ad	bronchial
17	chr14:68861000-68865400	Enhancers	Osteobl	bone
18	chr14:68861200-68866400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr14:68861200-68869400	Weak transcription	Liver	Liver
20	chr14:68861800-68864600	Weak transcription	Stomach Mucosa	stomach
21	chr14:68861800-68866800	Weak transcription	Psoas Muscle	Psoas
22	chr14:68861800-68871400	Weak transcription	Right Ventricle	heart
23	chr14:68862000-68865800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:68862000-68866800	Weak transcription	Brain Angular Gyrus	brain
25	chr14:68862000-68870400	Weak transcription	Brain Substantia Nigra	brain
26	chr14:68862200-68865200	Enhancers	Fetal Kidney	kidney
27	chr14:68862400-68864600	Weak transcription	Brain Anterior Caudate	brain
28	chr14:68862400-68864600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr14:68862400-68866000	Enhancers	Colon Smooth Muscle	Colon
30	chr14:68862400-68866400	Weak transcription	Dnd41	blood
31	chr14:68862400-68868000	Weak transcription	Aorta	Aorta
32	chr14:68862600-68864400	Enhancers	Hela-S3	cervix
33	chr14:68862600-68864600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr14:68862600-68864600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:68862600-68865600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:68862600-68866600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr14:68862600-68869800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr14:68862800-68864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr14:68862800-68865000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr14:68863000-68865400	Enhancers	HMEC	breast
41	chr14:68863200-68865400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr14:68863400-68865600	Enhancers	Fetal Intestine Small	intestine
43	chr14:68863600-68865000	Enhancers	HepG2	liver
44	chr14:68863600-68865400	Enhancers	Ovary	ovary
45	chr14:68863600-68865600	Enhancers	Fetal Lung	lung
46	chr14:68863600-68865600	Enhancers	Fetal Muscle Leg	muscle
47	chr14:68863600-68865800	Enhancers	Fetal Intestine Large	intestine
48	chr14:68863600-68865800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr14:68863600-68870000	Enhancers	Primary B cells from cord blood	blood
50	chr14:68863600-68877200	Enhancers	Primary B cells from peripheral blood	blood

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