Variant report

Variant	rs1200131
Chromosome Location	chr1:169078859-169078860
allele	A/G
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	GATA3	chr1:169078114-169079340	T-47D	breast:	n/a	n/a
2	POLR2A	chr1:169078795-169079417	H1-neurons	neurons:	n/a	n/a
3	RAD21	chr1:169078049-169079393	A549	lung:	n/a	chr1:169078627-169078641
4	SETDB1	chr1:169078650-169079170	U2OS	brain:	n/a	n/a
5	MAZ	chr1:169078529-169079441	HepG2	liver:	n/a	n/a
6	RAD21	chr1:169078140-169078869	A549	lung:	n/a	chr1:169078627-169078641
7	WRNIP1	chr1:169078018-169079251	GM12878	blood:	n/a	n/a
8	GATA3	chr1:169077923-169079727	A549	lung:	n/a	n/a
9	RAD21	chr1:169077989-169079396	HCT-116	colon:	n/a	chr1:169078627-169078641
10	GATA2	chr1:169078060-169080167	SH-SY5Y	brain:	n/a	n/a
11	FOSL2	chr1:169078097-169079875	A549	lung:	n/a	chr1:169079384-169079393
12	TAF1	chr1:169078746-169079292	A549	lung:	n/a	n/a
13	GATA2	chr1:169078613-169079644	HUVEC	blood vessel:	n/a	n/a
14	BCL3	chr1:169078529-169079411	A549	lung:	n/a	n/a
15	POLR2A	chr1:169074709-169082197	HepG2	liver:	n/a	n/a
16	SP1	chr1:169078054-169079801	A549	lung:	n/a	chr1:169078121-169078128 chr1:169079011-169079021 chr1:169079007-169079021 chr1:169078205-169078212 chr1:169079011-169079020
17	MAZ	chr1:169078121-169079352	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr1:169078164-169079347	HepG2	liver:	n/a	chr1:169078627-169078641
19	SIN3AK20	chr1:169078823-169079525	A549	lung:	n/a	n/a
20	FOSL2	chr1:169078849-169079478	A549	lung:	n/a	chr1:169079384-169079393
21	RAD21	chr1:169078511-169079301	IMR90	lung:	n/a	chr1:169078627-169078641
22	ATF3	chr1:169078757-169079518	A549	lung:	n/a	chr1:169079129-169079139 chr1:169079128-169079139 chr1:169079129-169079137 chr1:169079125-169079140 chr1:169079129-169079136 chr1:169079127-169079140 chr1:169079129-169079139
23	POLR2A	chr1:169078858-169079436	HepG2	liver:	n/a	n/a
24	KAP1	chr1:169078410-169079649	U2OS	brain:	n/a	n/a
25	NFYA	chr1:169078725-169079270	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:169078426-169079314	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:169078370-169079326	IMR90	lung:	n/a	n/a
28	RCOR1	chr1:169078211-169079312	HepG2	liver:	n/a	n/a
29	CEBPB	chr1:169078137-169079550	Hela-S3	cervix:	n/a	chr1:169079234-169079245
30	POLR2A	chr1:169078773-169079356	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr1:169078780-169078930	HVMF	connective:	n/a	n/a
32	SP1	chr1:169078489-169079534	HCT-116	colon:	n/a	chr1:169079011-169079021 chr1:169079007-169079021 chr1:169079011-169079020
33	POLR2A	chr1:169077925-169079433	Hela-S3	cervix:	n/a	n/a
34	GATA3	chr1:169078540-169079330	SH-SY5Y	brain:	n/a	n/a
35	HEY1	chr1:169078845-169079297	HepG2	liver:	n/a	chr1:169079129-169079138
36	RFX5	chr1:169078167-169079793	Hela-S3	cervix:	n/a	n/a
37	MAX	chr1:169077728-169079766	A549	lung:	n/a	chr1:169077893-169077902
38	MAX	chr1:169078082-169079482	A549	lung:	n/a	n/a
39	POLR2A	chr1:169078835-169079254	MCF10A-Er-Src	breast:	n/a	n/a
40	TAF1	chr1:169078838-169079360	H1-neurons	neurons:	n/a	n/a
41	GTF2F1	chr1:169078161-169079263	Hela-S3	cervix:	n/a	n/a
42	MBD4	chr1:169078847-169079483	HepG2	liver:	n/a	n/a
43	SMARCC1	chr1:169075987-169079359	Hela-S3	cervix:	n/a	n/a
44	SP1	chr1:169078857-169079463	HepG2	liver:	n/a	chr1:169079011-169079021 chr1:169079007-169079021 chr1:169079011-169079020
45	POLR2A	chr1:169078762-169079414	H1-neurons	neurons:	n/a	n/a
46	RAD21	chr1:169078165-169079370	A549	lung:	n/a	chr1:169078627-169078641
47	ARID3A	chr1:169078211-169079476	HepG2	liver:	n/a	n/a
48	CTCF	chr1:169078740-169078890	AG04450	lung:	n/a	n/a
49	ZNF263	chr1:169074720-169079408	HEK293-T-REx	kidney:	n/a	chr1:169077070-169077079 chr1:169077110-169077119
50	TCF7L2	chr1:169078522-169079422	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169045786..169047308-chr1:169077237..169079576,2	K562	blood:
2	chr1:168907357..168910687-chr1:169076812..169079423,3	MCF-7	breast:
3	chr1:169077517..169079516-chr22:21993938..21996836,2	MCF-7	breast:

Variant related genes	Relation type
ATP1B1	TF binding region
ENSG00000128228	Chromatin interaction
ENSG00000273342	Chromatin interaction
ENSG00000213063	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1200135	1.00[JPT][hapmap]
rs16861904	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs926517	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169074800-169079000	Active TSS	Fetal Kidney	kidney
2	chr1:169074800-169079200	Active TSS	Brain Hippocampus Middle	brain
3	chr1:169074800-169079400	Active TSS	Sigmoid Colon	Sigmoid Colon
4	chr1:169074800-169079600	Active TSS	Stomach Mucosa	stomach
5	chr1:169074800-169079800	Active TSS	Left Ventricle	heart
6	chr1:169074800-169080400	Active TSS	Right Ventricle	heart
7	chr1:169074800-169080800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr1:169075000-169079200	Active TSS	Esophagus	oesophagus
9	chr1:169075000-169079200	Active TSS	Fetal Intestine Large	intestine
10	chr1:169075000-169079200	Active TSS	Gastric	stomach
11	chr1:169075000-169079400	Active TSS	Colon Smooth Muscle	Colon
12	chr1:169075000-169080000	Active TSS	Brain Anterior Caudate	brain
13	chr1:169075000-169080000	Active TSS	GM12878-XiMat	blood
14	chr1:169075000-169080400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:169075000-169080600	Active TSS	Brain Cingulate Gyrus	brain
16	chr1:169075200-169079400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr1:169076000-169079400	Active TSS	Right Atrium	heart
18	chr1:169076400-169080800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:169076400-169081000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:169076600-169080200	Flanking Active TSS	NH-A	brain
21	chr1:169076600-169080600	Flanking Active TSS	HUVEC	blood vessel
22	chr1:169076800-169079400	Active TSS	Adipose Nuclei	Adipose
23	chr1:169076800-169079600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:169076800-169080000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr1:169076800-169080400	Active TSS	Brain Angular Gyrus	brain
26	chr1:169076800-169084800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:169077000-169079000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:169077000-169079200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:169077000-169079800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:169077000-169080000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:169077000-169080200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:169077200-169079000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:169077200-169079600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:169077200-169079800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr1:169077200-169079800	Active TSS	Colonic Mucosa	Colon
36	chr1:169077200-169080000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr1:169077200-169080200	Enhancers	NHDF-Ad	bronchial
38	chr1:169077200-169080600	Enhancers	Fetal Thymus	thymus
39	chr1:169077200-169082800	Weak transcription	Aorta	Aorta
40	chr1:169077200-169085200	Weak transcription	Spleen	Spleen
41	chr1:169077400-169079800	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr1:169077400-169079800	Flanking Active TSS	HMEC	breast
43	chr1:169077400-169079800	Flanking Active TSS	NHLF	lung
44	chr1:169077400-169080000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:169077400-169080000	Flanking Active TSS	Fetal Brain Male	brain
46	chr1:169077400-169080000	Flanking Active TSS	Hela-S3	cervix
47	chr1:169077400-169080200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr1:169077400-169080600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:169077400-169080800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:169077400-169081000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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