Variant report

Variant	rs4970944
Chromosome Location	chr1:151163317-151163318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151162065-151163320	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:151163316-151163366	HRPEpiC	eye:	n/a
2	chr1:151163316-151163366	HMEC	breast:	n/a
3	chr1:151163316-151163366	AG10803	skin:	n/a
4	chr1:151163316-151163366	ECC-1	luminal epithelium:	n/a
5	chr1:151163316-151163366	SKMC	muscle:	n/a
6	chr1:151163316-151163366	AG09309	skin:	n/a
7	chr1:151163316-151163366	IMR90	lung:	fetal
8	chr1:151163316-151163366	Jurkat	blood:	n/a
9	chr1:151163316-151163366	Caco-2	colon:	n/a
10	chr1:151163316-151163366	PANC-1	pancreas:	n/a
11	chr1:151163316-151163366	GM12891	blood:	n/a
12	chr1:151163316-151163366	HepG2	liver:	n/a
13	chr1:151163316-151163366	A549	lung:	n/a
14	chr1:151163316-151163366	PFSK-1	brain:	n/a
15	chr1:151163316-151163366	HUVEC	blood vessel:	n/a
16	chr1:151163316-151163366	HIPEpiC	eye:	n/a
17	chr1:151163316-151163366	T-47D	breast:	n/a
18	chr1:151163316-151163366	MCF-7	breast:	n/a
19	chr1:151163316-151163366	AG04450	lung:	fetal
20	chr1:151163316-151163366	BJ	skin:	n/a
21	chr1:151163316-151163366	NHDF-neo	bronchial:	n/a
22	chr1:151163316-151163366	GM19239	blood:	n/a
23	chr1:151163316-151163366	AG09319	gingival:	n/a
24	chr1:151163316-151163366	NT2-D1	testis:	n/a
25	chr1:151163316-151163366	MCF10A-Er-Src	breast:	n/a
26	chr1:151163316-151163366	AoSMC	blood vessel:	n/a
27	chr1:151163316-151163366	SK-N-SH_RA	brain:	n/a
28	chr1:151163316-151163366	H1-hESC	embryonic stem cell:	embryo
29	chr1:151163316-151163366	Hepatocyte	liver:	n/a
30	chr1:151163316-151163366	NB4	blood:	n/a
31	chr1:151163316-151163366	HAEpiC	amniotic membrane:	n/a
32	chr1:151163316-151163366	NH-A	brain:	n/a
33	chr1:151163316-151163366	K562	blood:	n/a
34	chr1:151163316-151163366	HEK293	kidney:	embryo
35	chr1:151163316-151163366	U87	brain:	n/a
36	chr1:151163316-151163366	ovcar-3	ovarian:	n/a
37	chr1:151163316-151163366	NHBE	bronchial:	n/a
38	chr1:151163316-151163366	HRE	kidney:	n/a
39	chr1:151163316-151163366	GM12892	blood:	n/a
40	chr1:151163316-151163366	CMK	blood:	n/a
41	chr1:151163316-151163366	BE2_C	brain:	n/a
42	chr1:151163316-151163366	HCT-116	colon:	n/a
43	chr1:151163316-151163366	SAEC	small airway:	n/a
44	chr1:151163316-151163366	PrEC	prostate:	n/a
45	chr1:151163316-151163366	HEEpiC	esophagus:	n/a
46	chr1:151163316-151163366	LNCaP	prostate:	n/a
47	chr1:151163316-151163366	HCPEpiC	choroid plexus:	n/a
48	chr1:151163316-151163366	HNPCEpiC	eye:	n/a
49	chr1:151163316-151163366	GM12878	blood:	n/a
50	chr1:151163316-151163366	AG04449	skin:	fetal

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151161317..151163856-chr1:151235890..151237991,2	MCF-7	breast:
2	chr1:151162193..151163907-chr1:151370731..151372764,2	MCF-7	breast:
3	chr1:151158002..151164153-chr1:151224298..151228623,7	MCF-7	breast:
4	chr1:151156826..151164982-chr1:151165389..151172985,25	MCF-7	breast:
5	chr1:151137906..151140464-chr1:151160968..151164864,6	K562	blood:
6	chr1:151161246..151164199-chr1:151225509..151227562,3	K562	blood:
7	chr1:151128359..151130289-chr1:151160585..151164269,3	K562	blood:
8	chr1:151161951..151163611-chr1:151344546..151346783,2	MCF-7	breast:
9	chr1:151162643..151164803-chr1:151253771..151256720,2	K562	blood:
10	chr1:151042897..151044564-chr1:151161784..151163721,2	MCF-7	breast:
11	chr1:151159807..151164370-chr1:151251735..151254419,4	MCF-7	breast:
12	chr1:151161136..151164205-chr1:151252246..151255061,3	K562	blood:
13	chr1:151144772..151148459-chr1:151159275..151164000,5	MCF-7	breast:
14	chr1:151137992..151140464-chr1:151160968..151164864,4	K562	blood:
15	chr1:151162057..151164706-chr1:151165181..151172008,8	K562	blood:
16	chr1:151136893..151140335-chr1:151160848..151164031,6	MCF-7	breast:

No data

Variant related genes	Relation type
VPS72	TF binding region
VPS72	CpG island
ENSG00000163156	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000163157	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000163154	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1056847	0.95[JPT][hapmap]
rs10749660	0.86[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];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10788801	0.90[JPT][hapmap]
rs10788803	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs10888406	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888408	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs10888409	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs10888410	0.85[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs11204785	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204791	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs11807075	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12022732	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12048670	0.81[EUR][1000 genomes]
rs12062719	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12080778	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12407426	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1536617	0.85[JPT][hapmap]
rs16827941	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16833079	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1752387	0.81[JPT][hapmap]
rs1892196	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2025900	0.86[JPT][hapmap]
rs2031797	0.85[JPT][hapmap]
rs2275900	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2769268	0.86[JPT][hapmap]
rs2769273	0.86[JPT][hapmap]
rs2800946	0.86[JPT][hapmap]
rs3811405	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs3811406	0.85[JPT][hapmap]
rs41302131	0.80[EUR][1000 genomes]
rs4246525	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4291501	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4520422	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];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4636463	0.92[GIH][hapmap];0.85[JPT][hapmap]
rs4970943	0.81[AMR][1000 genomes]
rs4970948	0.85[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs4971013	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]
rs4971015	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971016	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971018	0.85[JPT][hapmap]
rs4971021	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971023	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971025	0.81[EUR][1000 genomes]
rs4971026	0.83[EUR][1000 genomes]
rs4971027	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4971029	0.85[JPT][hapmap]
rs4971030	0.85[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs5022636	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs58323986	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817972	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587559	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];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587562	0.81[ASW][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap]
rs6678528	0.90[JPT][hapmap]
rs6681071	0.83[EUR][1000 genomes]
rs6681163	0.83[EUR][1000 genomes]
rs6683396	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6686402	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];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6695344	0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs6701325	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521064	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7527032	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];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7532935	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];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7539584	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];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7544947	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7545392	0.90[JPT][hapmap]
rs7552906	0.86[JPT][hapmap]
rs943637	0.85[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4970944	CTSS	cis	cerebellum	SCAN
rs4970944	SELENBP1	cis	cerebellum	SCAN
rs4970944	ARNT	cis	parietal	SCAN
rs4970944	PSMD4	cis	parietal	SCAN
rs4970944	MLLT11	cis	parietal	SCAN
rs4970944	CTSK	cis	cerebellum	SCAN
rs4970944	PSMD4	cis	cerebellum	SCAN
rs4970944	VPS45	cis	cerebellum	SCAN
rs4970944	MRPS21	cis	parietal	SCAN
rs4970944	ANKRD34A	cis	cerebellum	SCAN
rs4970944	FLG	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151161000-151163400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:151161000-151163400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:151161200-151163400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:151161400-151163400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:151161400-151163400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:151161400-151163400	Active TSS	Fetal Brain Female	brain
7	chr1:151161400-151163400	Active TSS	Psoas Muscle	Psoas
8	chr1:151161400-151163400	Active TSS	HMEC	breast
9	chr1:151161400-151163400	Active TSS	NHDF-Ad	bronchial
10	chr1:151161400-151164600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:151161600-151163400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:151161600-151163400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:151161600-151163400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:151161800-151163400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:151161800-151163400	Active TSS	Right Ventricle	heart
16	chr1:151162000-151163400	Active TSS	Brain Angular Gyrus	brain
17	chr1:151162000-151163400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:151162000-151163400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:151162000-151163400	Active TSS	Fetal Heart	heart
20	chr1:151162000-151163400	Active TSS	NHEK	skin
21	chr1:151162200-151163400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:151162200-151163400	Active TSS	Brain Anterior Caudate	brain
23	chr1:151162200-151163400	Active TSS	Colon Smooth Muscle	Colon
24	chr1:151162200-151163400	Active TSS	Duodenum Mucosa	Duodenum
25	chr1:151162200-151163400	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr1:151162200-151163400	Active TSS	Stomach Smooth Muscle	stomach
27	chr1:151162400-151163400	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr1:151162800-151163400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr1:151162800-151163400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:151162800-151167800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:151162800-151170200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:151162800-151170400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:151163000-151163400	Enhancers	Primary B cells from cord blood	blood
34	chr1:151163000-151163400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr1:151163000-151163400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr1:151163000-151163400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:151163000-151163400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:151163000-151163400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr1:151163000-151163400	Enhancers	NH-A	brain
40	chr1:151163000-151163600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr1:151163000-151163600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:151163000-151163600	Flanking Active TSS	Dnd41	blood
43	chr1:151163000-151170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:151163200-151163400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:151163200-151163400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:151163200-151163400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:151163200-151163400	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:151163200-151163400	Enhancers	Primary T cells from cord blood	blood
49	chr1:151163200-151163400	Enhancers	Primary T cells fromperipheralblood	blood
50	chr1:151163200-151163400	Enhancers	Primary hematopoietic stem cells	blood

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