Variant report

Variant	rs34001546
Chromosome Location	chr1:150459715-150459716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:548)
CpG islands
(count:122)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:548 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr1:150459491-150460350	ECC-1	luminal epithelium:	n/a	n/a
2	HA-E2F1	chr1:150459625-150460086	MCF-7	breast:	n/a	n/a
3	TAF1	chr1:150459398-150460325	A549	lung:	n/a	n/a
4	MYC	chr1:150459506-150460510	NB4	blood:	n/a	n/a
5	EBF1	chr1:150459537-150460006	GM12878	blood:	n/a	n/a
6	ELF1	chr1:150459514-150460063	K562	blood:	n/a	n/a
7	REST	chr1:150459492-150460115	HepG2	liver:	n/a	chr1:150460087-150460100
8	ZBTB7A	chr1:150459627-150459845	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:150459388-150460621	K562	blood:	n/a	n/a
10	PML	chr1:150459398-150460498	MCF-7	breast:	n/a	n/a
11	CTCF	chr1:150459648-150459950	GM12878	blood:	n/a	n/a
12	NR2F2	chr1:150459460-150460168	K562	blood:	n/a	n/a
13	POLR2A	chr1:150459544-150460086	HUVEC	blood vessel:	n/a	n/a
14	ZNF143	chr1:150459551-150460010	H1-hESC	embryonic stem cell:	n/a	n/a
15	SP2	chr1:150459533-150460080	H1-hESC	embryonic stem cell:	n/a	chr1:150459806-150459829
16	MEF2C	chr1:150459433-150459795	GM12878	blood:	n/a	chr1:150459651-150459662 chr1:150459650-150459664 chr1:150459648-150459669
17	TAF1	chr1:150459553-150460073	GM12878	blood:	n/a	n/a
18	MAX	chr1:150459599-150460044	H1-hESC	embryonic stem cell:	n/a	n/a
19	STAT3	chr1:150459574-150459935	Hela-S3	cervix:	n/a	n/a
20	GABPA	chr1:150459454-150460056	K562	blood:	n/a	n/a
21	MAFF	chr1:150459553-150459910	K562	blood:	n/a	n/a
22	NFYA	chr1:150459608-150460089	GM12878	blood:	n/a	n/a
23	SIN3AK20	chr1:150459527-150459805	PANC-1	pancreas:	n/a	n/a
24	JUND	chr1:150459597-150460177	A549	lung:	n/a	n/a
25	E2F4	chr1:150459606-150460049	MCF10A-Er-Src	breast:	n/a	n/a
26	GATA3	chr1:150459541-150460285	T-47D	breast:	n/a	chr1:150459571-150459581
27	TAF1	chr1:150459516-150460131	K562	blood:	n/a	n/a
28	TAF1	chr1:150459546-150460042	Hela-S3	cervix:	n/a	n/a
29	TAF1	chr1:150459568-150460142	H1-hESC	embryonic stem cell:	n/a	n/a
30	IRF1	chr1:150459568-150460076	K562	blood:	n/a	n/a
31	FOXA2	chr1:150459518-150460058	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:150459564-150460276	MCF-7	breast:	n/a	n/a
33	POLR2A	chr1:150459520-150460147	K562	blood:	n/a	n/a
34	TEAD4	chr1:150459429-150460048	K562	blood:	n/a	n/a
35	CEBPB	chr1:150459588-150459994	Hela-S3	cervix:	n/a	chr1:150459854-150459862
36	CTCF	chr1:150459680-150459950	GM12873	blood:	n/a	n/a
37	MAX	chr1:150459560-150460088	K562	blood:	n/a	n/a
38	GABPA	chr1:150459562-150460002	HepG2	liver:	n/a	n/a
39	CTCF	chr1:150459700-150459850	GM12878	blood:	n/a	n/a
40	TBP	chr1:150459535-150460084	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:150459640-150460458	GM12891	blood:	n/a	n/a
42	PBX3	chr1:150459441-150460195	SK-N-SH	brain:	n/a	chr1:150459808-150459828 chr1:150459854-150459863
43	RAD21	chr1:150459556-150460133	IMR90	lung:	n/a	n/a
44	SP1	chr1:150459473-150460109	K562	blood:	n/a	chr1:150459821-150459842
45	POLR2A	chr1:150459487-150460147	K562	blood:	n/a	n/a
46	YY1	chr1:150459561-150460102	K562	blood:	n/a	n/a
47	TCF7L2	chr1:150459617-150459948	PANC-1	pancreas:	n/a	n/a
48	MEF2C	chr1:150459410-150460129	GM12878	blood:	n/a	chr1:150459651-150459662 chr1:150459650-150459664 chr1:150459648-150459669
49	POLR2A	chr1:150459472-150460601	GM12891	blood:	n/a	n/a
50	USF1	chr1:150459474-150459903	A549	lung:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:150459698-150459748	NB4	blood:	n/a
2	chr1:150459698-150459748	GM19239	blood:	n/a
3	chr1:150459676-150459726	CMK	blood:	n/a
4	chr1:150459698-150459748	NHDF-neo	bronchial:	n/a
5	chr1:150459676-150459726	A549	lung:	n/a
6	chr1:150459676-150459726	GM06990	blood:	n/a
7	chr1:150459676-150459726	RPTEC	kidney:	n/a
8	chr1:150459698-150459748	U87	brain:	n/a
9	chr1:150459698-150459748	CMK	blood:	n/a
10	chr1:150459698-150459748	SKMC	muscle:	n/a
11	chr1:150459676-150459726	HIPEpiC	eye:	n/a
12	chr1:150459698-150459748	Jurkat	blood:	n/a
13	chr1:150459676-150459726	SAEC	small airway:	n/a
14	chr1:150459676-150459726	Hepatocyte	liver:	n/a
15	chr1:150459676-150459726	HUVEC	blood vessel:	n/a
16	chr1:150459676-150459726	HEEpiC	esophagus:	n/a
17	chr1:150459676-150459726	GM12891	blood:	n/a
18	chr1:150459698-150459748	HNPCEpiC	eye:	n/a
19	chr1:150459698-150459748	PANC-1	pancreas:	n/a
20	chr1:150459676-150459726	HNPCEpiC	eye:	n/a
21	chr1:150459676-150459726	HRE	kidney:	n/a
22	chr1:150459698-150459748	ECC-1	luminal epithelium:	n/a
23	chr1:150459676-150459726	HRCEpiC	kidney:	n/a
24	chr1:150459698-150459748	K562	blood:	n/a
25	chr1:150459698-150459748	GM12891	blood:	n/a
26	chr1:150459698-150459748	H1-hESC	embryonic stem cell:	embryo
27	chr1:150459698-150459748	HCT-116	colon:	n/a
28	chr1:150459698-150459748	HRPEpiC	eye:	n/a
29	chr1:150459698-150459748	HL-60	blood:	n/a
30	chr1:150459676-150459726	HAEpiC	amniotic membrane:	n/a
31	chr1:150459676-150459726	BE2_C	brain:	n/a
32	chr1:150459676-150459726	ECC-1	luminal epithelium:	n/a
33	chr1:150459698-150459748	HEK293	kidney:	embryo
34	chr1:150459698-150459748	AG09319	gingival:	n/a
35	chr1:150459698-150459748	HMEC	breast:	n/a
36	chr1:150459676-150459726	HMEC	breast:	n/a
37	chr1:150459698-150459748	HCM	heart:	n/a
38	chr1:150459676-150459726	SKMC	muscle:	n/a
39	chr1:150459698-150459748	LNCaP	prostate:	n/a
40	chr1:150459698-150459748	HCF	heart:	n/a
41	chr1:150459676-150459726	Hela-S3	cervix:	n/a
42	chr1:150459698-150459748	HRE	kidney:	n/a
43	chr1:150459698-150459748	T-47D	breast:	n/a
44	chr1:150459676-150459726	T-47D	breast:	n/a
45	chr1:150459698-150459748	IMR90	lung:	fetal
46	chr1:150459676-150459726	HCPEpiC	choroid plexus:	n/a
47	chr1:150459698-150459748	Hepatocyte	liver:	n/a
48	chr1:150459676-150459726	IMR90	lung:	fetal
49	chr1:150459676-150459726	ovcar-3	ovarian:	n/a
50	chr1:150459676-150459726	HepG2	liver:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr1:150456469..150460175-chr1:150533144..150536039,5	K562	blood:
2	chr1:150458168..150459777-chr1:150539728..150541445,2	MCF-7	breast:
3	chr1:150458483..150461483-chr1:150486453..150489390,6	MCF-7	breast:
4	chr1:150334215..150336170-chr1:150458883..150461226,2	K562	blood:
5	chr1:150458661..150461236-chr1:150531725..150536785,4	MCF-7	breast:
6	chr1:150459313..150460106-chr17:16284149..16284677,2	HCT-116	colon:
7	chr1:150458274..150463765-chr1:150483214..150490747,8	K562	blood:
8	chr1:150459417..150461989-chr1:150549858..150552620,3	MCF-7	breast:
9	chr1:150457915..150461156-chr1:150532058..150534752,4	MCF-7	breast:
10	chr1:113160681..113163117-chr1:150458124..150460105,2	MCF-7	breast:
11	chr1:150459018..150460856-chr1:150519254..150522007,2	MCF-7	breast:
12	chr1:150458615..150462130-chr1:150550221..150553114,4	K562	blood:
13	chr1:150455871..150459967-chr1:150528884..150531556,5	MCF-7	breast:
14	chr1:150458113..150460742-chr1:150599904..150603804,4	MCF-7	breast:
15	chr1:150335716..150337496-chr1:150457670..150459977,2	MCF-7	breast:
16	chr1:150458065..150461622-chr1:150486691..150490573,5	MCF-7	breast:
17	chr1:150458118..150461224-chr1:150521416..150523335,4	K562	blood:
18	chr1:150459471..150461027-chr1:150601141..150603564,2	K562	blood:
19	chr1:150458161..150459880-chr1:150550348..150552555,2	MCF-7	breast:
20	chr1:150457583..150461907-chr1:150523895..150528793,6	MCF-7	breast:
21	chr1:150458453..150462100-chr1:150463666..150466292,4	K562	blood:
22	chr1:150458028..150460943-chr1:150462500..150464059,2	K562	blood:
23	chr1:150458473..150461317-chr1:150523404..150525508,2	MCF-7	breast:
24	chr1:150458426..150460384-chr1:150464250..150466250,2	K562	blood:
25	chr1:150459274..150461316-chr1:150480408..150482138,3	K562	blood:

No data

Variant related genes	Relation type
TARS2	TF binding region
TARS2	CpG island
ENSG00000225996	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000237781	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143369	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000170315	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000264553	Chromatin interaction
ENSG00000228126	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11799813	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs11800656	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801190	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801255	0.93[EUR][1000 genomes]
rs11802612	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803448	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806171	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs11807119	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809332	1.00[ASN][1000 genomes]
rs11810419	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap]
rs12718416	0.96[EUR][1000 genomes]
rs12723364	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724450	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729727	1.00[ASN][1000 genomes]
rs12730265	1.00[ASN][1000 genomes]
rs12735903	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12736584	1.00[ASN][1000 genomes]
rs12743761	1.00[ASN][1000 genomes]
rs12745672	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12747619	1.00[CEU][hapmap]
rs12749958	1.00[ASN][1000 genomes]
rs12756583	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759551	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495360	1.00[ASN][1000 genomes]
rs34233130	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34307322	1.00[ASN][1000 genomes]
rs34347495	1.00[ASN][1000 genomes]
rs34448981	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34514406	1.00[ASN][1000 genomes]
rs34542152	1.00[ASN][1000 genomes]
rs34609268	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34629240	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34696422	0.85[EUR][1000 genomes]
rs34964511	1.00[ASN][1000 genomes]
rs35094010	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35347210	1.00[ASN][1000 genomes]
rs35437473	1.00[ASN][1000 genomes]
rs35762205	1.00[ASN][1000 genomes]
rs35839143	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35935423	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs56214117	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57323357	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58427317	1.00[ASN][1000 genomes]
rs58853199	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71515775	1.00[ASN][1000 genomes]
rs71622688	1.00[ASN][1000 genomes]
rs71622689	1.00[ASN][1000 genomes]
rs71622694	1.00[ASN][1000 genomes]
rs71622695	1.00[ASN][1000 genomes]
rs71622696	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71622697	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71622698	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71622702	1.00[ASN][1000 genomes]
rs74124663	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74124686	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517003	1.00[ASN][1000 genomes]
rs7535275	1.00[ASN][1000 genomes]
rs7542068	0.89[MKK][hapmap]
rs7546610	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150459000-150460200	Active TSS	Brain Hippocampus Middle	brain
2	chr1:150459200-150460000	Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:150459200-150460000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:150459200-150460200	Active TSS	Psoas Muscle	Psoas
5	chr1:150459200-150460200	Active TSS	Thymus	Thymus
6	chr1:150459200-150460400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:150459200-150460400	Active TSS	Right Atrium	heart
8	chr1:150459200-150460600	Active TSS	Aorta	Aorta
9	chr1:150459200-150460600	Active TSS	GM12878-XiMat	blood
10	chr1:150459200-150460800	Active TSS	Fetal Brain Female	brain
11	chr1:150459400-150459800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr1:150459400-150460000	Active TSS	Primary monocytes fromperipheralblood	blood
13	chr1:150459400-150460000	Active TSS	Primary T cells fromperipheralblood	blood
14	chr1:150459400-150460000	Active TSS	Primary hematopoietic stem cells	blood
15	chr1:150459400-150460000	Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr1:150459400-150460000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr1:150459400-150460000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:150459400-150460000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:150459400-150460000	Active TSS	Liver	Liver
20	chr1:150459400-150460000	Bivalent/Poised TSS	HepG2	liver
21	chr1:150459400-150460000	Active TSS	HMEC	breast
22	chr1:150459400-150460000	Active TSS	Monocytes-CD14+_RO01746	blood
23	chr1:150459400-150460200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:150459400-150460200	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr1:150459400-150460200	Active TSS	Primary B cells from cord blood	blood
26	chr1:150459400-150460200	Active TSS	Primary B cells from peripheral blood	blood
27	chr1:150459400-150460200	Active TSS	Primary T cells from cord blood	blood
28	chr1:150459400-150460200	Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:150459400-150460200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:150459400-150460200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:150459400-150460200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr1:150459400-150460200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:150459400-150460200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:150459400-150460200	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr1:150459400-150460200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:150459400-150460200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:150459400-150460200	Active TSS	Brain Angular Gyrus	brain
38	chr1:150459400-150460200	Active TSS	Brain Anterior Caudate	brain
39	chr1:150459400-150460200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr1:150459400-150460200	Active TSS	Brain Substantia Nigra	brain
41	chr1:150459400-150460200	Active TSS	Duodenum Mucosa	Duodenum
42	chr1:150459400-150460200	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr1:150459400-150460200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr1:150459400-150460200	Active TSS	Fetal Lung	lung
45	chr1:150459400-150460200	Active TSS	Fetal Muscle Leg	muscle
46	chr1:150459400-150460200	Active TSS	Placenta	Placenta
47	chr1:150459400-150460200	Active TSS	Fetal Stomach	stomach
48	chr1:150459400-150460200	Active TSS	Fetal Thymus	thymus
49	chr1:150459400-150460200	Active TSS	Left Ventricle	heart
50	chr1:150459400-150460200	Active TSS	Pancreas	Pancrea

The 2.0 version of rSNPBase

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