Variant report

Variant	rs1390489
Chromosome Location	chr1:152161103-152161104
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:152161014-152161635	MCF-7	breast:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
2	CTCF	chr1:152161011-152161392	HepG2	liver:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
3	ZNF143	chr1:152161096-152161427	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOXA1	chr1:152161070-152161452	T-47D	breast:	n/a	n/a
5	SMC3	chr1:152161040-152161469	GM12878	blood:	n/a	chr1:152161240-152161254 chr1:152161244-152161254
6	CTCF	chr1:152161055-152161471	K562	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
7	CTCF	chr1:152161043-152161428	K562	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
8	CTCF	chr1:152160964-152161570	K562	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
9	CTCF	chr1:152161053-152161383	SK-N-SH_RA	brain:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
10	FOXA1	chr1:152161077-152161383	T-47D	breast:	n/a	n/a
11	GABPA	chr1:152161009-152162101	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr1:152161045-152161485	IMR90	lung:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
13	CTCF	chr1:152160976-152161546	HCT-116	colon:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
14	ZNF143	chr1:152161086-152161386	K562	blood:	n/a	n/a
15	KAP1	chr1:152161070-152161582	HEK293	kidney:	n/a	n/a
16	RAD21	chr1:152161085-152161443	IMR90	lung:	n/a	chr1:152161239-152161258 chr1:152161244-152161254 chr1:152161240-152161254
17	RAD21	chr1:152161080-152161477	H1-hESC	embryonic stem cell:	n/a	chr1:152161239-152161258 chr1:152161244-152161254 chr1:152161240-152161254
18	CTCF	chr1:152161090-152161406	GM10266	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
19	CTCF	chr1:152161099-152161630	GM19238	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
20	MAX	chr1:152160938-152162843	A549	lung:	n/a	chr1:152162503-152162510 chr1:152162500-152162510
21	RAD21	chr1:152161003-152161468	ECC-1	luminal epithelium:	n/a	chr1:152161239-152161258 chr1:152161244-152161254 chr1:152161240-152161254
22	CTCF	chr1:152161080-152161230	A549	lung:	n/a	n/a
23	CTCF	chr1:152161040-152161360	ECC-1	luminal epithelium:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
24	CTCF	chr1:152161006-152161469	A549	lung:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
25	SMC3	chr1:152161080-152161463	K562	blood:	n/a	chr1:152161240-152161254 chr1:152161244-152161254
26	CTCF	chr1:152161054-152161469	T-47D	breast:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
27	CTCF	chr1:152160990-152161557	HCT-116	colon:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
28	RAD21	chr1:152161020-152161411	A549	lung:	n/a	chr1:152161239-152161258 chr1:152161244-152161254 chr1:152161240-152161254
29	CTCF	chr1:152161097-152161391	K562	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
30	FOXA2	chr1:152160920-152161582	A549	lung:	n/a	n/a
31	CTCF	chr1:152161061-152161364	K562	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
32	CTCF	chr1:152161060-152161210	HCM	heart:	n/a	n/a
33	CTCF	chr1:152161039-152161496	GM12878	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
34	CTCF	chr1:152161100-152161428	A549	lung:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
35	CTCF	chr1:152161099-152161400	MCF-7	breast:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
36	CTCF	chr1:152161060-152161210	HAc	cerebellar:	n/a	n/a
37	MAX	chr1:152161014-152162727	A549	lung:	n/a	chr1:152162503-152162510 chr1:152162500-152162510
38	RAD21	chr1:152161096-152161402	H1-hESC	embryonic stem cell:	n/a	chr1:152161239-152161258 chr1:152161244-152161254 chr1:152161240-152161254
39	CTCF	chr1:152161045-152161406	H1-hESC	embryonic stem cell:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
40	CTCF	chr1:152160980-152161422	T-47D	breast:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
41	ZNF143	chr1:152161070-152161445	GM12878	blood:	n/a	n/a
42	CTCF	chr1:152161068-152161417	GM13977	blood:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
43	CTCF	chr1:152161092-152161412	Spleen_OC	spleen:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
44	CTCF	chr1:152160886-152161743	SK-N-SH	brain:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
45	RAD21	chr1:152161048-152161512	MCF-7	breast:	n/a	chr1:152161239-152161258 chr1:152161244-152161254 chr1:152161240-152161254
46	TCF12	chr1:152160933-152162220	A549	lung:	n/a	chr1:152161238-152161248
47	CTCF	chr1:152161101-152161396	HUVEC	blood vessel:	n/a	chr1:152161238-152161256 chr1:152161241-152161254 chr1:152161243-152161253 chr1:152161239-152161255 chr1:152161240-152161261 chr1:152161241-152161254 chr1:152161241-152161250
48	YY1	chr1:152161091-152161332	SK-N-SH_RA	brain:	n/a	n/a
49	CTCF	chr1:152161100-152161250	WI-38	lung:	n/a	chr1:152161241-152161250
50	GABPA	chr1:152161071-152162255	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:152025124..152025656-chr1:152161097..152161675,2	MCF-7	breast:
2	chr1:152019527..152021275-chr1:152158923..152161325,2	MCF-7	breast:
3	chr1:152160966..152161616-chr1:152433035..152433995,2	MCF-7	breast:
4	chr1:152160950..152161743-chr1:152199424..152200319,5	MCF-7	breast:
5	chr1:152160624..152161417-chr1:152199475..152200038,4	MCF-7	breast:
6	chr1:152161041..152161774-chr1:152423855..152424586,2	MCF-7	breast:
7	chr1:152160815..152161721-chr1:152320660..152321540,3	MCF-7	breast:
8	chr1:152160802..152161752-chr1:152430569..152431282,4	MCF-7	breast:
9	chr1:152024690..152025212-chr1:152160729..152161691,2	MCF-7	breast:
10	chr1:152160785..152161519-chr1:152413069..152413968,2	K562	blood:
11	chr1:152023608..152024485-chr1:152160789..152161681,3	MCF-7	breast:

Variant related genes	Relation type
FLG-AS1	TF binding region
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10494273	0.85[CHD][hapmap]
rs10749668	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10749669	0.90[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs10788822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10788824	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs10788826	0.87[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs10888466	0.90[AFR][1000 genomes]
rs10888467	0.82[AFR][1000 genomes]
rs11588174	0.90[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs12063165	0.81[AFR][1000 genomes]
rs12116736	0.84[AFR][1000 genomes]
rs12728908	1.00[CHB][hapmap]
rs12728920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1496045	0.83[LWK][hapmap];0.89[YRI][hapmap]
rs1496050	0.89[AFR][1000 genomes]
rs1496051	0.89[AFR][1000 genomes]
rs1552995	0.82[AFR][1000 genomes]
rs1552996	0.81[AFR][1000 genomes]
rs16833867	0.85[CHD][hapmap]
rs16833966	0.85[CHD][hapmap]
rs1858481	0.85[CHD][hapmap];1.00[MEX][hapmap]
rs2496250	1.00[CHB][hapmap]
rs3126065	1.00[MEX][hapmap]
rs3126087	1.00[MEX][hapmap]
rs3134871	0.85[CHD][hapmap];1.00[MEX][hapmap]
rs3134872	1.00[MEX][hapmap]
rs4845423	0.90[LWK][hapmap];0.96[YRI][hapmap]
rs4845733	0.89[AFR][1000 genomes]
rs4845736	0.90[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs4845740	0.81[AFR][1000 genomes]
rs4845745	0.84[LWK][hapmap];0.89[YRI][hapmap]
rs868303	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv547854	chr1:152145661-152165878	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152152200-152161200	Weak transcription	Right Atrium	heart
2	chr1:152154400-152161400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:152156000-152161200	Weak transcription	A549	lung
4	chr1:152156000-152161200	Weak transcription	HSMM	muscle
5	chr1:152157800-152161200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:152158000-152161200	Weak transcription	NHDF-Ad	bronchial
7	chr1:152158200-152161400	Weak transcription	NH-A	brain
8	chr1:152158600-152161200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:152158800-152161200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:152159000-152161200	Weak transcription	Ovary	ovary
11	chr1:152159800-152161200	Weak transcription	Esophagus	oesophagus
12	chr1:152159800-152161200	Weak transcription	HMEC	breast
13	chr1:152159800-152161200	Weak transcription	Osteobl	bone
14	chr1:152160000-152161200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:152160200-152161200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:152160200-152161200	Weak transcription	NHEK	skin
17	chr1:152160400-152161200	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:152160600-152162000	Weak transcription	Hela-S3	cervix
19	chr1:152161000-152161200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr1:152161000-152161200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr1:152161000-152161200	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr1:152161000-152161200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:152161000-152161200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:152161000-152161200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:152161000-152161200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:152161000-152161200	Enhancers	Brain Anterior Caudate	brain
27	chr1:152161000-152161200	Enhancers	Brain Substantia Nigra	brain
28	chr1:152161000-152161200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr1:152161000-152161200	Flanking Active TSS	Fetal Kidney	kidney
30	chr1:152161000-152161200	Enhancers	Lung	lung
31	chr1:152161000-152161200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
32	chr1:152161000-152161200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:152161000-152161400	Enhancers	Fetal Heart	heart
34	chr1:152161000-152161400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
35	chr1:152161000-152162000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:152161000-152162200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:152161000-152162200	Active TSS	Primary T cells from cord blood	blood
38	chr1:152161000-152162200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:152161000-152162200	Active TSS	Right Ventricle	heart
40	chr1:152161000-152162600	Active TSS	Stomach Smooth Muscle	stomach

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