Variant report

Variant	rs2073656
Chromosome Location	chr1:161011355-161011356
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:129)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:129 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:161011330-161011558	LNCaP	prostate:	n/a	n/a
2	CTCF	chr1:161011272-161011572	Spleen_OC	spleen:	n/a	n/a
3	CTCF	chr1:161011340-161011490	HVMF	connective:	n/a	n/a
4	CTCF	chr1:161011303-161011616	GM19239	blood:	n/a	n/a
5	CTCF	chr1:161011322-161011574	GM10266	blood:	n/a	n/a
6	RAD21	chr1:161011276-161011612	SK-N-SH_RA	brain:	n/a	n/a
7	RAD21	chr1:161011266-161011573	HepG2	liver:	n/a	n/a
8	SMC3	chr1:161011276-161011630	Hela-S3	cervix:	n/a	n/a
9	JUND	chr1:161011191-161011596	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr1:161011179-161011713	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr1:161011336-161011555	GM20000	blood:	n/a	n/a
12	CTCF	chr1:161011340-161011490	GM12873	blood:	n/a	n/a
13	RAD21	chr1:161011227-161011597	A549	lung:	n/a	n/a
14	SMC3	chr1:161011281-161011612	K562	blood:	n/a	n/a
15	CTCF	chr1:161011327-161011552	LNCaP	prostate:	n/a	n/a
16	CTCF	chr1:161011322-161011601	MCF-7	breast:	n/a	n/a
17	CTCF	chr1:161011321-161011606	A549	lung:	n/a	n/a
18	CTCF	chr1:161011297-161011617	NHEK	skin:	n/a	n/a
19	CTCF	chr1:161011309-161011606	Fibrobl	skin:	n/a	n/a
20	RAD21	chr1:161011323-161011637	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr1:161011276-161011580	GM12892	blood:	n/a	n/a
22	CTCF	chr1:161011313-161011586	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr1:161011232-161011660	GM12878	blood:	n/a	n/a
24	CTCF	chr1:161011260-161011595	K562	blood:	n/a	n/a
25	CTCF	chr1:161011315-161011575	MCF-7	breast:	n/a	n/a
26	CTCF	chr1:161011268-161011591	T-47D	breast:	n/a	n/a
27	CTCF	chr1:161011322-161011585	A549	lung:	n/a	n/a
28	RAD21	chr1:161011267-161011637	IMR90	lung:	n/a	n/a
29	RAD21	chr1:161011203-161011694	ECC-1	luminal epithelium:	n/a	n/a
30	CTCF	chr1:161011302-161011610	Gliobla	brain:	n/a	n/a
31	CTCF	chr1:161011340-161011490	NHLF	lung:	n/a	n/a
32	CTCF	chr1:161011340-161011490	RPTEC	kidney:	n/a	n/a
33	CTCF	chr1:161011089-161011861	SK-N-SH	brain:	n/a	n/a
34	RAD21	chr1:161011263-161011581	GM12878	blood:	n/a	n/a
35	CTCF	chr1:161011343-161011531	A549	lung:	n/a	n/a
36	CTCF	chr1:161011276-161011723	K562	blood:	n/a	n/a
37	RAD21	chr1:161011250-161011642	A549	lung:	n/a	n/a
38	CTCF	chr1:161011233-161011675	MCF-7	breast:	n/a	n/a
39	POLR2A	chr1:161011316-161011626	K562	blood:	n/a	n/a
40	HDAC2	chr1:161011353-161011573	K562	blood:	n/a	n/a
41	CTCF	chr1:161011320-161011470	GM12872	blood:	n/a	n/a
42	ZMIZ1	chr1:161011338-161011511	K562	blood:	n/a	n/a
43	CTCF	chr1:161011305-161011585	K562	blood:	n/a	n/a
44	CTCF	chr1:161011340-161011490	GM12866	blood:	n/a	n/a
45	CTCF	chr1:161011280-161011430	HAc	cerebellar:	n/a	n/a
46	POLR2A	chr1:161011212-161011655	K562	blood:	n/a	n/a
47	CTCF	chr1:161011300-161011615	GM12891	blood:	n/a	n/a
48	RAD21	chr1:161011262-161011615	HepG2	liver:	n/a	n/a
49	RAD21	chr1:161011278-161011637	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr1:161011320-161011470	GM12870	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
2	chr1:161011228..161012764-chr1:161122593..161124625,2	K562	blood:
3	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
4	chr1:161005808..161012985-chr1:161064732..161070101,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270149	TF binding region
USF1	TF binding region
TSTD1	TF binding region
ENSG00000162755	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000143222	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1044478	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs1062826	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs1062827	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs11265540	0.83[AMR][1000 genomes]
rs11265542	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11799478	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11799521	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11801586	0.81[AMR][1000 genomes]
rs11801591	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs11802727	1.00[YRI][hapmap]
rs11807930	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes]
rs12401336	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12403334	0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs12408778	0.82[AMR][1000 genomes]
rs12565932	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs1556519	1.00[YRI][hapmap]
rs17384360	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17388108	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1806774	0.86[AMR][1000 genomes]
rs2073655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243427	0.84[AMR][1000 genomes]
rs2247459	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes]
rs2247596	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs2247671	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs2247790	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes]
rs2251597	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2251728	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2297219	0.89[AMR][1000 genomes]
rs2297220	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs2297221	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs2297222	0.86[CEU][hapmap];0.89[AMR][1000 genomes]
rs2481080	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs2481081	0.91[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes]
rs2481083	0.84[AMR][1000 genomes]
rs2481084	0.91[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2481085	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2483145	0.84[AMR][1000 genomes]
rs2774274	0.84[AMR][1000 genomes]
rs2988726	0.84[AMR][1000 genomes]
rs3119321	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3737785	0.87[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes]
rs3737787	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267947	0.89[AMR][1000 genomes]
rs41267949	0.89[AMR][1000 genomes]
rs41267951	0.89[AMR][1000 genomes]
rs41269993	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4339888	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55728374	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60315407	0.80[AMR][1000 genomes]
rs61803664	0.89[AMR][1000 genomes]
rs61803671	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61803672	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72712854	0.86[AMR][1000 genomes]
rs812741	0.84[AMR][1000 genomes]
rs836	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes]
rs869985	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv947201	chr1:161006051-161013276	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv872492	chr1:161009523-161013152	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2073656	FCRL1	cis	cerebellum	SCAN
rs2073656	RXFP4	cis	parietal	SCAN
rs2073656	OR10J5	cis	cerebellum	SCAN
rs2073656	PAQR6	cis	cerebellum	SCAN
rs2073656	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161007000-161013400	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:161007400-161013400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:161007400-161013400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:161007400-161013400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:161007400-161013400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:161007600-161013400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:161008000-161013200	Strong transcription	A549	lung
8	chr1:161008000-161013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:161008200-161013000	Strong transcription	NHLF	lung
10	chr1:161008600-161011400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:161008800-161012600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:161008800-161013000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:161008800-161013400	Strong transcription	Brain Cingulate Gyrus	brain
14	chr1:161008800-161014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:161009000-161011800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:161009000-161012400	Weak transcription	Psoas Muscle	Psoas
17	chr1:161009000-161012600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:161009000-161012800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:161009000-161012800	Strong transcription	Adipose Nuclei	Adipose
20	chr1:161009000-161013200	Strong transcription	Osteobl	bone
21	chr1:161009000-161013400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:161009000-161013400	Strong transcription	Fetal Stomach	stomach
23	chr1:161009000-161014000	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr1:161009200-161012400	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr1:161009200-161012600	Strong transcription	Colon Smooth Muscle	Colon
26	chr1:161009200-161012800	Strong transcription	Aorta	Aorta
27	chr1:161009200-161012800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:161009200-161013000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:161009200-161013000	Strong transcription	Brain Substantia Nigra	brain
30	chr1:161009200-161013000	Strong transcription	HSMMtube	muscle
31	chr1:161009200-161013000	Strong transcription	HUVEC	blood vessel
32	chr1:161009200-161013200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:161009200-161013200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:161009200-161013200	Strong transcription	Fetal Kidney	kidney
35	chr1:161009200-161013200	Strong transcription	Hela-S3	cervix
36	chr1:161009200-161013200	Strong transcription	HepG2	liver
37	chr1:161009200-161013200	Strong transcription	NH-A	brain
38	chr1:161009200-161013200	Strong transcription	NHDF-Ad	bronchial
39	chr1:161009200-161013200	Strong transcription	NHEK	skin
40	chr1:161009200-161013400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:161009200-161013400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:161009200-161013400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:161009200-161013400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:161009200-161013400	Strong transcription	Brain Angular Gyrus	brain
45	chr1:161009200-161013400	Strong transcription	Brain Anterior Caudate	brain
46	chr1:161009200-161013400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:161009400-161012000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:161009400-161012800	Strong transcription	Brain Hippocampus Middle	brain
49	chr1:161009400-161012800	Strong transcription	Esophagus	oesophagus
50	chr1:161009400-161012800	Strong transcription	Left Ventricle	heart

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