Variant report

Variant	rs3211056
Chromosome Location	chr14:24909475-24909476
allele	C/G
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24801605..24806320-chr14:24904693..24909744,5	K562	blood:
2	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
3	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
4	chr14:24909091..24910881-chr4:187644537..187646251,2	MCF-7	breast:
5	chr14:24872891..24878220-chr14:24906746..24909504,4	MCF-7	breast:
6	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
7	chr14:24738558..24740532-chr14:24907754..24910468,2	MCF-7	breast:
8	chr14:24796552..24799266-chr14:24908909..24911628,3	K562	blood:
9	chr14:24783396..24785005-chr14:24908424..24911111,2	K562	blood:
10	chr14:24698279..24701346-chr14:24909291..24912292,3	MCF-7	breast:
11	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
12	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
13	chr14:24860779..24862341-chr14:24908273..24910091,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213903	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000207141	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000083857	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000100968	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10083368	0.87[JPT][hapmap]
rs10083382	0.87[JPT][hapmap]
rs10083509	0.87[JPT][hapmap]
rs10129168	0.87[JPT][hapmap]
rs10133116	0.88[JPT][hapmap]
rs10133998	0.88[JPT][hapmap]
rs10140911	0.87[JPT][hapmap]
rs10143987	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158704	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158706	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158707	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621453	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621715	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626161	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627132	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11627137	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11628143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433369	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12433402	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12879887	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12882878	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12884447	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12897925	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473725	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17103735	0.87[JPT][hapmap]
rs17103743	0.87[JPT][hapmap]
rs17103869	0.88[JPT][hapmap]
rs17103960	0.87[JPT][hapmap]
rs17104012	0.87[JPT][hapmap]
rs17184822	0.92[CEU][hapmap]
rs1951123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951137	0.81[JPT][hapmap]
rs1956891	0.80[YRI][hapmap]
rs1956892	0.87[YRI][hapmap]
rs1956893	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1956896	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1956898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956899	0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1956901	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956903	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073335	0.81[JPT][hapmap]
rs2273628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277489	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2332333	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332334	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3742521	0.87[JPT][hapmap]
rs3809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814810	0.86[JPT][hapmap]
rs4278673	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4290409	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4400972	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4433735	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4981518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981521	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981522	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981523	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982916	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982918	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4982919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982924	0.87[YRI][hapmap]
rs4982925	0.86[YRI][hapmap]
rs4982926	0.87[YRI][hapmap]
rs712487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7142374	0.85[JPT][hapmap]
rs7143327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7144118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7148891	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7149743	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7151530	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7157349	0.86[JPT][hapmap]
rs737245	0.88[JPT][hapmap]
rs737246	0.87[JPT][hapmap]
rs737247	0.88[JPT][hapmap]
rs737248	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8008300	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8013991	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs8015535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1053330	chr14:24908047-24993666	Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	n/a
4	nsv482171	chr14:24908974-24912007	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	40 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3211056	SDR39U1	cis	Whole Blood	GTEx
rs3211056	SDR39U1	cis	Muscle Skeletal	GTEx
rs3211056	C14orf124	Cis_1M	lymphoblastoid	RTeQTL
rs3211056	SDR39U1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24900200-24911000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:24900600-24910600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr14:24901400-24910200	Strong transcription	Aorta	Aorta
4	chr14:24901600-24909800	Weak transcription	Fetal Heart	heart
5	chr14:24901600-24910400	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr14:24901800-24910000	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:24902400-24909800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr14:24902400-24910200	Strong transcription	A549	lung
9	chr14:24902400-24910600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr14:24903000-24910000	Weak transcription	Psoas Muscle	Psoas
11	chr14:24903000-24910000	Strong transcription	NHEK	skin
12	chr14:24903400-24909600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:24904200-24910200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
14	chr14:24904400-24910400	Genic enhancers	Adipose Nuclei	Adipose
15	chr14:24904600-24910400	Strong transcription	Fetal Lung	lung
16	chr14:24904800-24910400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:24905400-24910000	Genic enhancers	Primary monocytes fromperipheralblood	blood
18	chr14:24905400-24910600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:24905400-24910600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:24905400-24911000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr14:24905800-24910600	Strong transcription	HSMM	muscle
22	chr14:24906000-24910000	Strong transcription	Fetal Intestine Small	intestine
23	chr14:24906000-24910200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr14:24906000-24910400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr14:24906000-24910400	Strong transcription	Osteobl	bone
26	chr14:24906200-24909800	Strong transcription	HepG2	liver
27	chr14:24906200-24910400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:24906200-24910400	Genic enhancers	Spleen	Spleen
29	chr14:24906200-24910600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr14:24906400-24909600	Strong transcription	Brain Angular Gyrus	brain
31	chr14:24906400-24909800	Strong transcription	Brain Cingulate Gyrus	brain
32	chr14:24906400-24909800	Strong transcription	Brain Substantia Nigra	brain
33	chr14:24906400-24909800	Strong transcription	Fetal Intestine Large	intestine
34	chr14:24906400-24910200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr14:24906400-24910400	Strong transcription	Rectal Smooth Muscle	rectum
36	chr14:24906400-24910600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr14:24906600-24910200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr14:24906600-24910200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr14:24906800-24909600	Strong transcription	Fetal Brain Male	brain
40	chr14:24906800-24910000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:24906800-24910000	Strong transcription	Fetal Stomach	stomach
42	chr14:24906800-24910200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr14:24906800-24910400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr14:24907000-24909600	Strong transcription	Brain Anterior Caudate	brain
45	chr14:24907000-24909800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr14:24907000-24909800	Strong transcription	GM12878-XiMat	blood
47	chr14:24907000-24910000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr14:24907000-24910400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr14:24907000-24911000	Weak transcription	Right Atrium	heart
50	chr14:24907200-24909800	Strong transcription	Fetal Brain Female	brain

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