Variant report

Variant	rs4898785
Chromosome Location	chr14:38343968-38343969
allele	G/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:13)
LncRNA
region (count:1)
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	chr14:38178183..38179217-chr14:38343472..38344512,5	MCF-7	breast:
2	chr14:37715448..37716190-chr14:38343588..38344540,3	MCF-7	breast:
3	chr14:38055655..38059490-chr14:38342768..38346428,4	MCF-7	breast:
4	chr14:37715320..37716132-chr14:38343587..38344326,2	MCF-7	breast:
5	chr14:38338833..38341519-chr14:38342499..38345279,2	MCF-7	breast:
6	chr14:38339276..38342707-chr14:38343768..38347145,3	MCF-7	breast:
7	chr14:38177834..38178487-chr14:38343555..38344210,2	MCF-7	breast:
8	chr14:38062426..38066513-chr14:38338443..38346839,18	MCF-7	breast:
9	chr14:38178359..38181904-chr14:38339541..38344216,4	MCF-7	breast:
10	chr14:38178580..38179381-chr14:38343573..38344582,8	MCF-7	breast:
11	chr14:38343955..38346094-chr14:38346760..38348457,2	MCF-7	breast:
12	chr14:38060189..38065879-chr14:38339920..38349339,20	MCF-7	breast:
13	chr14:37720959..37721697-chr14:38343187..38344314,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MIPOL1-6	chr14:38343586-38344006	NONHSAT036473

No data

Variant related genes	Relation type
ENSG00000139865	Chromatin interaction
ENSG00000129514	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10134624	0.93[CEU][hapmap]
rs10140719	0.92[CEU][hapmap]
rs10145136	0.93[CEU][hapmap]
rs10146385	0.93[CEU][hapmap]
rs10483495	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10872905	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1113092	0.92[CEU][hapmap]
rs11156973	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11156974	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11621735	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11622986	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs1170022	0.93[CEU][hapmap]
rs1170023	0.84[CEU][hapmap]
rs1170025	0.92[CEU][hapmap]
rs1170028	0.93[CEU][hapmap]
rs1170029	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs1170030	0.89[CEU][hapmap];0.80[YRI][hapmap]
rs1170031	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs11851837	0.89[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12432452	0.92[CEU][hapmap]
rs12435640	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12590816	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12882516	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs12883466	0.91[GIH][hapmap]
rs17107343	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs17179919	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs17554993	0.93[CEU][hapmap];0.82[TSI][hapmap]
rs1952787	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs1952788	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1952790	0.93[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1958693	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1958694	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1959676	0.93[CEU][hapmap]
rs2150322	0.88[CEU][hapmap];0.81[CHD][hapmap]
rs2150323	0.80[YRI][hapmap]
rs2183531	0.89[CEU][hapmap];0.81[CHD][hapmap]
rs35272292	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809444	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143919	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4322573	0.85[CEU][hapmap];0.81[CHD][hapmap]
rs4597229	0.85[CEU][hapmap]
rs4901412	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4901413	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4901421	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4901422	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4901423	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6571829	0.89[CEU][hapmap];0.86[YRI][hapmap]
rs6571830	0.87[CEU][hapmap]
rs7155891	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8005651	0.93[CEU][hapmap]
rs8005895	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8013747	0.89[CEU][hapmap];0.80[YRI][hapmap]
rs8014896	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs8015738	0.92[CEU][hapmap]
rs9322983	0.93[CEU][hapmap];0.82[TSI][hapmap]
rs954881	0.93[CEU][hapmap]
rs9788473	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9788476	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]

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	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	nsv1051120	chr14:38294270-38436127	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv542046	chr14:38294270-38436127	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv564386	chr14:38311855-38365605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4898785	C14orf19	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38340400-38344000	Weak transcription	Adipose Nuclei	Adipose
2	chr14:38340400-38344000	Weak transcription	Fetal Muscle Leg	muscle
3	chr14:38340600-38344000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:38343600-38344000	Enhancers	NHLF	lung
5	chr14:38343600-38344200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr14:38343600-38344200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr14:38343600-38344200	Enhancers	Gastric	stomach
8	chr14:38343600-38344400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr14:38343600-38344400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr14:38343600-38344400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr14:38343600-38344400	Enhancers	Liver	Liver
12	chr14:38343600-38344400	Enhancers	Colon Smooth Muscle	Colon
13	chr14:38343600-38344400	Enhancers	Fetal Intestine Small	intestine
14	chr14:38343600-38344400	Enhancers	Stomach Smooth Muscle	stomach
15	chr14:38343600-38344400	Flanking Active TSS	HepG2	liver
16	chr14:38343600-38344400	Enhancers	NHDF-Ad	bronchial
17	chr14:38343600-38344600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr14:38343600-38344800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr14:38343800-38344000	Flanking Active TSS	Stomach Mucosa	stomach
20	chr14:38343800-38344000	Flanking Active TSS	Hela-S3	cervix
21	chr14:38343800-38344200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr14:38343800-38344200	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr14:38343800-38344200	Enhancers	Esophagus	oesophagus
24	chr14:38343800-38344200	Enhancers	Left Ventricle	heart
25	chr14:38343800-38344200	Enhancers	Pancreas	Pancrea
26	chr14:38343800-38344200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr14:38343800-38344200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr14:38343800-38344200	Active TSS	A549	lung
29	chr14:38343800-38344400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:38343800-38344400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr14:38343800-38344400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr14:38343800-38344400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:38343800-38344400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr14:38343800-38344400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr14:38343800-38344400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr14:38343800-38344400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr14:38343800-38344400	Enhancers	Fetal Lung	lung
38	chr14:38343800-38344400	Enhancers	Dnd41	blood
39	chr14:38343800-38344400	Enhancers	HMEC	breast
40	chr14:38343800-38344400	Enhancers	HSMM	muscle
41	chr14:38343800-38344400	Enhancers	HUVEC	blood vessel
42	chr14:38343800-38344400	Enhancers	NH-A	brain
43	chr14:38343800-38344400	Enhancers	NHEK	skin
44	chr14:38343800-38344600	Enhancers	Muscle Satellite Cultured Cells	--

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