Variant report

Variant	rs2072331
Chromosome Location	chr17:19575721-19575722
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	JUND	chr17:19575325-19575961	HepG2	liver:	n/a	n/a
2	RAD21	chr17:19575250-19576086	HepG2	liver:	n/a	chr17:19575953-19575966
3	RAD21	chr17:19575710-19576041	SK-N-SH_RA	brain:	n/a	chr17:19575953-19575966
4	SP1	chr17:19575251-19575826	HepG2	liver:	n/a	n/a
5	HDAC2	chr17:19575201-19575862	HepG2	liver:	n/a	n/a
6	FOXA2	chr17:19575220-19575998	HepG2	liver:	n/a	n/a
7	HNF4A	chr17:19575277-19575818	HepG2	liver:	n/a	chr17:19575779-19575791 chr17:19575553-19575568 chr17:19575649-19575657
8	TCF7L2	chr17:19575260-19575898	HepG2	liver:	n/a	chr17:19575627-19575643 chr17:19575630-19575639 chr17:19575616-19575625 chr17:19575612-19575628 chr17:19575627-19575643 chr17:19575628-19575642 chr17:19575612-19575628 chr17:19575631-19575641
9	ARID3A	chr17:19575285-19576052	HepG2	liver:	n/a	n/a
10	MBD4	chr17:19574998-19576071	HepG2	liver:	n/a	n/a
11	ELF1	chr17:19575437-19576029	HepG2	liver:	n/a	chr17:19575896-19575907
12	FOXA1	chr17:19575298-19576000	HepG2	liver:	n/a	n/a
13	NFIC	chr17:19575222-19575974	HepG2	liver:	n/a	n/a
14	RAD21	chr17:19575665-19576084	A549	lung:	n/a	chr17:19575953-19575966
15	FOXA1	chr17:19575257-19575786	HepG2	liver:	n/a	n/a
16	MYBL2	chr17:19575139-19575830	HepG2	liver:	n/a	n/a
17	HNF4A	chr17:19575375-19575768	HepG2	liver:	n/a	chr17:19575553-19575568 chr17:19575649-19575657
18	RAD21	chr17:19575716-19576086	MCF-7	breast:	n/a	chr17:19575953-19575966
19	POLR2A	chr17:19575692-19575863	HepG2	liver:	n/a	n/a
20	FOXA1	chr17:19575203-19575847	HepG2	liver:	n/a	n/a
21	EP300	chr17:19575285-19575821	HepG2	liver:	n/a	n/a
22	SMC3	chr17:19575348-19576088	HepG2	liver:	n/a	n/a
23	TCF12	chr17:19575179-19575735	ECC-1	luminal epithelium:	n/a	n/a
24	RCOR1	chr17:19575294-19575972	HepG2	liver:	n/a	n/a
25	TEAD4	chr17:19575133-19575880	HepG2	liver:	n/a	n/a
26	RAD21	chr17:19575600-19576104	MCF-7	breast:	n/a	chr17:19575953-19575966
27	CEBPB	chr17:19575320-19575786	HepG2	liver:	n/a	chr17:19575699-19575711
28	HNF4G	chr17:19575319-19575836	HepG2	liver:	n/a	chr17:19575779-19575791 chr17:19575649-19575657
29	FOXA1	chr17:19575226-19575818	HepG2	liver:	n/a	n/a
30	RAD21	chr17:19575645-19576184	SK-N-SH	brain:	n/a	chr17:19575953-19575966
31	CTCF	chr17:19575720-19575970	HAc	cerebellar:	n/a	n/a
32	EP300	chr17:19575085-19576021	HepG2	liver:	n/a	chr17:19575898-19575907
33	RAD21	chr17:19575643-19576101	HCT-116	colon:	n/a	chr17:19575953-19575966
34	CEBPB	chr17:19574862-19575817	HepG2	liver:	n/a	chr17:19575699-19575711 chr17:19574983-19574996
35	RAD21	chr17:19575244-19576125	HepG2	liver:	n/a	chr17:19575953-19575966
36	RXRA	chr17:19575301-19575789	HepG2	liver:	n/a	n/a
37	EP300	chr17:19575271-19575846	HepG2	liver:	n/a	n/a
38	CEBPB	chr17:19575256-19575733	HepG2	liver:	n/a	chr17:19575699-19575711
39	JUN	chr17:19575443-19575823	HepG2	liver:	n/a	n/a
40	CTCF	chr17:19575704-19576160	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19265895..19266829-chr17:19575547..19576368,3	MCF-7	breast:
2	chr17:19550468..19552548-chr17:19574981..19577039,2	MCF-7	breast:
3	chr17:19565101..19568606-chr17:19573068..19575796,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC115989.1.1-6	chr17:19575665-19575744	NONHSAT146516

Variant related genes	Relation type
ALDH3A2	TF binding region
ENSG00000108641	Chromatin interaction
ENSG00000252349	Chromatin interaction
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004491	0.84[CHD][hapmap]
rs1025904	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1034896	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204407	0.84[CHD][hapmap]
rs11650399	0.94[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11653348	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11658227	0.84[CHB][hapmap]
rs12453452	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453474	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12602112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12603959	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12937179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938816	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949521	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1800869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806922	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2072332	0.84[CHD][hapmap]
rs2072333	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245724	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2386144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2891952	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34943952	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35797108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35852749	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3786038	0.82[CHD][hapmap]
rs4598966	0.82[EUR][1000 genomes]
rs4646793	0.84[CHD][hapmap]
rs4646797	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646798	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925041	0.82[CHD][hapmap]
rs66462929	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71369434	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223468	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72840391	0.82[AMR][1000 genomes]
rs7503517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8064748	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8068713	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8073053	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8080672	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs962801	0.84[CHD][hapmap]
rs9797254	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9909440	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv907865	chr17:19558722-19575721	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2072331	SMCR7	cis	cerebellum	SCAN
rs2072331	TOM1L2	cis	parietal	SCAN
rs2072331	ALDH3A2	cis	lymphoblastoid	seeQTL
rs2072331	ALDH3A2	cis	cerebellum	SCAN
rs2072331	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs2072331	MED9	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
5	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
7	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:19559800-19577200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:19564000-19581000	Weak transcription	Thymus	Thymus
11	chr17:19565400-19575800	Strong transcription	Fetal Stomach	stomach
12	chr17:19567000-19575800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:19567600-19578600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:19567600-19584800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:19567800-19578600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:19568400-19581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
18	chr17:19569000-19582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:19569400-19577000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:19569600-19578600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr17:19569600-19579000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:19569600-19584000	Weak transcription	Placenta	Placenta
23	chr17:19569800-19578600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:19569800-19578600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:19569800-19591000	Weak transcription	Fetal Brain Male	brain
26	chr17:19570000-19578800	Weak transcription	Colonic Mucosa	Colon
27	chr17:19570000-19579200	Weak transcription	Aorta	Aorta
28	chr17:19572400-19576600	Strong transcription	Brain Germinal Matrix	brain
29	chr17:19572600-19582800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr17:19572800-19576200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:19572800-19580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:19572800-19583000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr17:19573000-19576000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:19573600-19576000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:19574000-19576000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr17:19574000-19576200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr17:19574200-19575800	Genic enhancers	Adipose Nuclei	Adipose
38	chr17:19574200-19576000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr17:19574200-19576000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:19574200-19576000	Genic enhancers	Brain Anterior Caudate	brain
41	chr17:19574200-19576000	Genic enhancers	Brain Inferior Temporal Lobe	brain
42	chr17:19574200-19576000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:19574200-19576000	Enhancers	Brain Substantia Nigra	brain
44	chr17:19574200-19576000	Enhancers	HSMMtube	muscle
45	chr17:19574200-19576200	Genic enhancers	Fetal Muscle Leg	muscle
46	chr17:19574200-19576400	Genic enhancers	Brain Cingulate Gyrus	brain
47	chr17:19574200-19576600	Strong transcription	Primary T cells from cord blood	blood
48	chr17:19574200-19577200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr17:19574200-19577800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr17:19574200-19579000	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links