Variant report

Variant	rs2735591
Chromosome Location	chr1:85744472-85744473
allele	C/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	MAX	chr1:85744399-85745029	SK-N-SH	brain:	n/a	n/a
2	STAT5A	chr1:85744371-85744959	K562	blood:	n/a	n/a
3	POLR2A	chr1:85744456-85745017	MCF10A-Er-Src	breast:	n/a	n/a
4	JUN	chr1:85744425-85745740	K562	blood:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
5	JUND	chr1:85744329-85745186	HCT-116	colon:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
6	FOS	chr1:85744472-85744944	MCF10A-Er-Src	breast:	n/a	chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
7	RXRA	chr1:85744404-85745081	SK-N-SH	brain:	n/a	chr1:85744539-85744552 chr1:85744540-85744551 chr1:85744539-85744552
8	POLR2A	chr1:85744460-85744944	K562	blood:	n/a	n/a
9	E2F4	chr1:85744465-85744940	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:85744472-85745015	HUVEC	blood vessel:	n/a	chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
11	FOSL2	chr1:85744423-85745009	A549	lung:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
12	TEAD4	chr1:85744328-85745031	K562	blood:	n/a	n/a
13	PBX3	chr1:85744331-85745079	SK-N-SH	brain:	n/a	n/a
14	TBL1XR1	chr1:85744403-85745019	K562	blood:	n/a	n/a
15	JUND	chr1:85744322-85745112	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
16	POLR2A	chr1:85744463-85744928	K562	blood:	n/a	n/a
17	GATA3	chr1:85744342-85745131	SK-N-SH	brain:	n/a	chr1:85744620-85744630 chr1:85744486-85744497 chr1:85744596-85744603
18	JUND	chr1:85744410-85745015	K562	blood:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
19	SP1	chr1:85744309-85745181	HCT-116	colon:	n/a	chr1:85744679-85744700
20	TCF12	chr1:85744438-85745122	SK-N-SH	brain:	n/a	n/a
21	TCF12	chr1:85744313-85745100	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:85744386-85745051	SK-N-SH	brain:	n/a	n/a
23	STAT5A	chr1:85744378-85744835	K562	blood:	n/a	n/a
24	SP1	chr1:85744424-85744865	A549	lung:	n/a	chr1:85744679-85744700
25	MAX	chr1:85744394-85745107	A549	lung:	n/a	n/a
26	FOSL1	chr1:85744325-85745062	HCT-116	colon:	n/a	chr1:85744729-85744740 chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
27	GATA3	chr1:85744303-85745020	A549	lung:	n/a	chr1:85744620-85744630 chr1:85744486-85744497 chr1:85744596-85744603
28	POLR2A	chr1:85744426-85744985	HCT-116	colon:	n/a	n/a
29	FOSL1	chr1:85744351-85745217	HCT-116	colon:	n/a	chr1:85744729-85744740 chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
30	TAF1	chr1:85744415-85744970	PFSK-1	brain:	n/a	n/a
31	ARID3A	chr1:85744451-85744938	K562	blood:	n/a	n/a
32	JUND	chr1:85744309-85745294	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
33	MAX	chr1:85744469-85744938	K562	blood:	n/a	n/a
34	FOS	chr1:85744449-85744950	MCF10A-Er-Src	breast:	n/a	chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
35	JUND	chr1:85744324-85745112	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
36	KAP1	chr1:85744469-85745162	U2OS	brain:	n/a	n/a
37	EP300	chr1:85744431-85745007	MCF-7	breast:	n/a	n/a
38	SP1	chr1:85744385-85745215	HCT-116	colon:	n/a	chr1:85744679-85744700
39	FOSL2	chr1:85744395-85745095	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
40	FOSL2	chr1:85744458-85745014	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
41	PML	chr1:85744426-85745090	K562	blood:	n/a	n/a
42	POLR2A	chr1:85744278-85745155	U87	brain:	n/a	n/a
43	CUX1	chr1:85744389-85745107	K562	blood:	n/a	n/a
44	MAZ	chr1:85744460-85745002	K562	blood:	n/a	n/a
45	PBX3	chr1:85744399-85745058	SK-N-SH	brain:	n/a	n/a
46	MAX	chr1:85744425-85745040	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr1:85744436-85744975	U87	brain:	n/a	n/a
48	GATA2	chr1:85744401-85745017	HUVEC	blood vessel:	n/a	chr1:85744620-85744630 chr1:85744486-85744497 chr1:85744596-85744603
49	SIN3AK20	chr1:85744318-85745121	MCF-7	breast:	n/a	n/a
50	CBX3	chr1:85744378-85745025	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85742187..85745018-chr1:85749555..85753087,3	K562	blood:
2	chr1:85743465..85746291-chr1:85746776..85749038,2	MCF-7	breast:
3	chr1:85741905..85744580-chr1:85747619..85751624,6	K562	blood:
4	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

Variant related genes	Relation type
BCL10	TF binding region
ENSG00000264380	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10493762	0.82[JPT][hapmap]
rs11161574	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11583836	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12065422	0.91[GIH][hapmap]
rs17122364	0.82[JPT][hapmap]
rs17123650	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2054238	0.81[JPT][hapmap]
rs2252408	0.96[ASN][1000 genomes]
rs233101	0.84[CHB][hapmap]
rs233102	0.80[CHB][hapmap]
rs2647396	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735587	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735588	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2735592	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2735594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4907139	0.83[JPT][hapmap]
rs4949926	0.87[ASN][1000 genomes]
rs6663690	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6671589	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6693365	0.98[ASN][1000 genomes]
rs7530433	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2735591	C1orf52	cis	cerebellum	SCAN
rs2735591	C1orf180	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742200-85744600	Weak transcription	Gastric	stomach
2	chr1:85742200-85744800	Weak transcription	Spleen	Spleen
3	chr1:85742800-85744600	Weak transcription	Pancreas	Pancrea
4	chr1:85742800-85744600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:85742800-85744600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:85742800-85763000	Weak transcription	Ovary	ovary
7	chr1:85743000-85744600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:85743000-85744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:85743000-85744600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:85743000-85744600	Weak transcription	Fetal Kidney	kidney
11	chr1:85743000-85744600	Enhancers	HUVEC	blood vessel
12	chr1:85743000-85744800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:85743000-85745400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:85743000-85746000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:85743000-85747400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:85743000-85749200	Weak transcription	Fetal Stomach	stomach
17	chr1:85743000-85749200	Weak transcription	Psoas Muscle	Psoas
18	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
19	chr1:85743200-85744600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:85743200-85744600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:85743200-85744600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:85743200-85744600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:85743200-85744600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:85743200-85744600	Enhancers	Hela-S3	cervix
25	chr1:85743200-85744800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:85743200-85744800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:85743200-85744800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:85743200-85744800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:85743200-85744800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:85743200-85744800	Weak transcription	Colonic Mucosa	Colon
31	chr1:85743200-85744800	Weak transcription	Esophagus	oesophagus
32	chr1:85743200-85744800	Weak transcription	Placenta	Placenta
33	chr1:85743200-85744800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:85743200-85744800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:85743200-85744800	Weak transcription	Right Ventricle	heart
36	chr1:85743200-85744800	Enhancers	HMEC	breast
37	chr1:85743200-85744800	Enhancers	NHEK	skin
38	chr1:85743200-85745000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:85743200-85745000	Weak transcription	Left Ventricle	heart
40	chr1:85743200-85745200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:85743200-85745200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:85743200-85745200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:85743200-85745800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:85743200-85747800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:85743200-85747800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:85743200-85747800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:85743200-85748000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:85743200-85748200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:85743200-85752000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:85743400-85744600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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