Variant report

Variant	rs4971013
Chromosome Location	chr1:151173113-151173114
allele	A/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:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	1:151171193-151178589..1:151411623-151426875	GM12878	blood:
2	chr1:151171270..151173891-chr1:151252685..151255060,3	K562	blood:
3	1:151171193-151178589..1:151246650-151254384	GM12878	blood:
4	chr1:151169497..151174843-chr1:151224312..151231181,18	MCF-7	breast:
5	chr1:151171256..151175527-chr1:151178181..151182275,7	MCF-7	breast:
6	chr1:151138200..151140251-chr1:151173020..151175658,2	MCF-7	breast:
7	1:151171193-151178589..1:151333184-151350267	GM12878	blood:
8	1:151171193-151178589..1:151219411-151234038	GM12878	blood:
9	chr1:151171485..151173202-chr17:57182944..57185192,2	MCF-7	breast:
10	1:151171193-151178589..1:151254384-151268403	Hela-S3	cervix:
11	1:151171193-151178589..1:151516085-151535167	GM12878	blood:
12	chr1:151170967..151173717-chr1:151426450..151428273,2	MCF-7	breast:
13	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
14	1:151171193-151178589..1:151203965-151215310	GM12878	blood:
15	1:151171193-151178589..1:151368336-151375897	Hela-S3	cervix:
16	chr1:151168724..151174586-chr1:151252405..151256834,10	MCF-7	breast:
17	1:151171193-151178589..1:151496437-151509688	Hela-S3	cervix:
18	chr1:151172835..151174401-chr1:151177247..151179111,2	K562	blood:
19	chr1:151170887..151173171-chr1:151225503..151227858,2	K562	blood:
20	1:151171193-151178589..1:151270864-151283078	K562	blood:
21	chr1:151170794..151172311-chr1:151172927..151175239,2	MCF-7	breast:
22	1:151171193-151178589..1:151618750-151636526	Hela-S3	cervix:
23	chr1:151169931..151174343-chr1:151224824..151227591,5	MCF-7	breast:
24	chr1:151169798..151173171-chr1:151225503..151227858,3	K562	blood:
25	1:151171193-151178589..1:151309061-151322694	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000163155	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000265753	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000143398	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1056847	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs10749660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10788801	0.90[JPT][hapmap]
rs10788803	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs10888406	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10888408	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888409	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs10888410	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs11204785	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204791	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11807075	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12022732	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040384	0.83[ASN][1000 genomes]
rs12048670	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12062719	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080778	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12407426	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1536617	0.85[JPT][hapmap]
rs16827941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16833079	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1752387	0.80[JPT][hapmap]
rs1892196	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2025900	0.85[JPT][hapmap]
rs2031797	0.85[JPT][hapmap]
rs2275900	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2769268	0.85[JPT][hapmap]
rs2769273	0.85[JPT][hapmap]
rs2800946	0.85[JPT][hapmap]
rs3811405	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs3811406	0.85[JPT][hapmap]
rs41302131	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4246525	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs4291501	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4520422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4636463	0.92[GIH][hapmap];0.84[JPT][hapmap]
rs4970944	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4970948	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4971015	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971016	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971018	0.84[JPT][hapmap]
rs4971021	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971025	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971026	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971027	0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4971029	0.85[JPT][hapmap]
rs4971030	0.90[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs5022636	0.83[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs58323986	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61817972	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587562	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6678528	0.90[JPT][hapmap]
rs6681071	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6681163	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6683396	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6686402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695344	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6701325	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7521064	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7527032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545392	0.90[JPT][hapmap]
rs7552906	0.86[JPT][hapmap]
rs943637	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4971013	ARNT	cis	parietal	SCAN
rs4971013	CTSS	cis	cerebellum	SCAN
rs4971013	FLG	cis	cerebellum	SCAN
rs4971013	PSMD4	cis	parietal	SCAN
rs4971013	PSMD4	cis	brain	BrainEAC
rs4971013	SELENBP1	cis	cerebellum	SCAN
rs4971013	PSMD4	cis	cerebellum	SCAN
rs4971013	MRPS21	cis	parietal	SCAN
rs4971013	ANKRD34A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151170200-151173200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:151170200-151173200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:151170200-151173200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:151170200-151173200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:151170200-151173200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:151170200-151173200	Active TSS	Right Ventricle	heart
7	chr1:151170200-151173400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:151170200-151173600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:151170400-151173200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:151170400-151173200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:151170400-151173200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:151170400-151173200	Active TSS	Aorta	Aorta
13	chr1:151170400-151173200	Active TSS	Ovary	ovary
14	chr1:151170600-151173200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:151170600-151173200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:151170600-151173200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:151170600-151173200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:151170600-151173200	Active TSS	Left Ventricle	heart
19	chr1:151170600-151173600	Active TSS	A549	lung
20	chr1:151170600-151174200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:151170600-151174200	Active TSS	GM12878-XiMat	blood
22	chr1:151170600-151174600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:151170600-151174600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:151170800-151173200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:151170800-151173200	Active TSS	Placenta	Placenta
26	chr1:151170800-151173200	Active TSS	HSMMtube	muscle
27	chr1:151170800-151173200	Active TSS	NHDF-Ad	bronchial
28	chr1:151170800-151173400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:151170800-151173400	Active TSS	NH-A	brain
30	chr1:151170800-151173600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:151170800-151173600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:151170800-151173600	Active TSS	Muscle Satellite Cultured Cells	--
33	chr1:151170800-151173600	Active TSS	HSMM	muscle
34	chr1:151170800-151173600	Active TSS	NHLF	lung
35	chr1:151170800-151173800	Active TSS	HMEC	breast
36	chr1:151171600-151173200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:151171800-151173200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:151171800-151173200	Flanking Active TSS	Fetal Thymus	thymus
39	chr1:151171800-151174400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:151172000-151173200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:151172000-151173200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr1:151172000-151173200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:151172000-151173600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:151172200-151173200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr1:151172200-151173200	Flanking Active TSS	Thymus	Thymus
46	chr1:151172200-151173200	Flanking Active TSS	Osteobl	bone
47	chr1:151172400-151174000	Enhancers	Small Intestine	intestine
48	chr1:151172400-151174600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:151172600-151173200	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr1:151172600-151173200	Active TSS	Fetal Heart	heart

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