Variant report

Variant	rs734663
Chromosome Location	chr2:39743876-39743877
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	TEAD4	chr2:39741859-39744517	HepG2	liver:	n/a	n/a
2	RAD21	chr2:39742783-39744133	HepG2	liver:	n/a	chr2:39743395-39743407
3	FOXA1	chr2:39742241-39744195	HepG2	liver:	n/a	n/a
4	FOXA2	chr2:39743116-39744257	HepG2	liver:	n/a	n/a
5	SIN3A	chr2:39743522-39743927	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:39743816-39744129	HepG2	liver:	n/a	n/a
7	TEAD4	chr2:39743480-39743880	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr2:39742465-39744118	HepG2	liver:	n/a	chr2:39742697-39742710 chr2:39743395-39743407
9	SP1	chr2:39743472-39743960	H1-hESC	embryonic stem cell:	n/a	n/a
10	RCOR1	chr2:39743873-39743993	Hela-S3	cervix:	n/a	n/a
11	ELF1	chr2:39743524-39743980	HepG2	liver:	n/a	n/a
12	GATA2	chr2:39743648-39744314	HUVEC	blood vessel:	n/a	chr2:39743983-39743991
13	POLR2A	chr2:39742555-39744239	HepG2	liver:	n/a	n/a
14	REST	chr2:39742237-39744268	HepG2	liver:	n/a	n/a
15	GATA3	chr2:39743810-39744191	MCF-7	breast:	n/a	chr2:39743983-39743991
16	EP300	chr2:39742238-39744188	HepG2	liver:	n/a	chr2:39743536-39743550
17	FOXA1	chr2:39742633-39744113	HepG2	liver:	n/a	n/a
18	FOXA1	chr2:39742288-39744191	HepG2	liver:	n/a	n/a
19	SP1	chr2:39742317-39744188	HepG2	liver:	n/a	n/a
20	FOS	chr2:39743711-39744497	HUVEC	blood vessel:	n/a	chr2:39744473-39744483
21	POLR2A	chr2:39743591-39744084	HUVEC	blood vessel:	n/a	n/a
22	NFIC	chr2:39741998-39745286	HepG2	liver:	n/a	n/a
23	JUN	chr2:39743619-39744376	HUVEC	blood vessel:	n/a	n/a
24	FOXA2	chr2:39741986-39744260	HepG2	liver:	n/a	n/a
25	RAD21	chr2:39743042-39744430	SK-N-SH	brain:	n/a	chr2:39743395-39743407
26	TBP	chr2:39742462-39744131	HepG2	liver:	n/a	n/a
27	TCF12	chr2:39743494-39744072	H1-hESC	embryonic stem cell:	n/a	n/a
28	HNF4A	chr2:39743525-39743890	HepG2	liver:	n/a	n/a
29	GATA3	chr2:39743609-39744227	MCF-7	breast:	n/a	chr2:39743983-39743991
30	JUND	chr2:39743514-39743933	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:39743054-39744149	HepG2	liver:	n/a	n/a
32	POLR2A	chr2:39743519-39744269	HUVEC	blood vessel:	n/a	n/a
33	EP300	chr2:39742330-39744126	HepG2	liver:	n/a	chr2:39743536-39743550
34	CTBP2	chr2:39743544-39744160	H1-hESC	embryonic stem cell:	n/a	n/a
35	HDAC2	chr2:39742393-39744256	HepG2	liver:	n/a	chr2:39743531-39743545 chr2:39743532-39743546 chr2:39743323-39743337
36	YY1	chr2:39743595-39744200	HepG2	liver:	n/a	n/a
37	MBD4	chr2:39742350-39744171	HepG2	liver:	n/a	n/a
38	NFIC	chr2:39742340-39744390	HepG2	liver:	n/a	n/a
39	POLR2A	chr2:39742497-39744395	HepG2	liver:	n/a	n/a
40	ELF1	chr2:39743189-39744111	HepG2	liver:	n/a	n/a
41	NR2F2	chr2:39742322-39744177	HepG2	liver:	n/a	chr2:39742616-39742631
42	SMC3	chr2:39742716-39743978	HepG2	liver:	n/a	n/a
43	RAD21	chr2:39743353-39743885	A549	lung:	n/a	chr2:39743395-39743407
44	MBD4	chr2:39742388-39744225	HepG2	liver:	n/a	n/a
45	MXI1	chr2:39742554-39744180	HepG2	liver:	n/a	n/a
46	FOXA1	chr2:39742347-39744117	HepG2	liver:	n/a	n/a
47	MYBL2	chr2:39741995-39744529	HepG2	liver:	n/a	n/a
48	RAD21	chr2:39743324-39743950	H1-hESC	embryonic stem cell:	n/a	chr2:39743395-39743407
49	POLR2A	chr2:39743443-39744252	HUVEC	blood vessel:	n/a	n/a
50	HEY1	chr2:39742425-39744601	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-1	chr2:39743555-39743909	ENSG00000231312.2

Variant related genes	Relation type
ENSG00000231312	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10180761	0.89[ASW][hapmap]
rs10191970	0.85[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11124686	0.89[EUR][1000 genomes]
rs11896239	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13027520	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13391377	0.85[ASN][1000 genomes]
rs1526024	0.88[EUR][1000 genomes]
rs17473802	1.00[ASW][hapmap]
rs17532603	0.82[CEU][hapmap]
rs2888602	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs35377016	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4670282	0.83[ASN][1000 genomes]
rs4670285	0.88[JPT][hapmap]
rs4670943	0.82[ASN][1000 genomes]
rs56337010	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6741839	0.88[EUR][1000 genomes]
rs6753798	0.85[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs72803112	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72803115	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7594967	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs734663	MAP4K3	cis	cerebellum	SCAN
rs734663	HEATR5B	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39712400-39748600	Weak transcription	Aorta	Aorta
2	chr2:39724800-39750600	Weak transcription	Gastric	stomach
3	chr2:39734600-39745000	Enhancers	Adipose Nuclei	Adipose
4	chr2:39734600-39746000	Enhancers	Fetal Heart	heart
5	chr2:39735000-39744800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:39736400-39745000	Enhancers	Right Atrium	heart
7	chr2:39736400-39745000	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:39737000-39744800	Enhancers	Fetal Muscle Leg	muscle
9	chr2:39737000-39745000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:39738000-39745000	Enhancers	Duodenum Mucosa	Duodenum
11	chr2:39739800-39744200	Enhancers	K562	blood
12	chr2:39739800-39745600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:39740600-39745000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:39740800-39745000	Enhancers	Left Ventricle	heart
15	chr2:39741400-39744000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:39741400-39745000	Enhancers	Spleen	Spleen
17	chr2:39741600-39744000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:39741600-39744000	Weak transcription	Stomach Mucosa	stomach
19	chr2:39741600-39744400	Enhancers	Fetal Intestine Small	intestine
20	chr2:39741600-39748600	Weak transcription	NHDF-Ad	bronchial
21	chr2:39741800-39745600	Flanking Active TSS	HepG2	liver
22	chr2:39742000-39745000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr2:39742000-39745000	Enhancers	Liver	Liver
24	chr2:39742200-39744600	Enhancers	H9 Cell Line	embryonic stem cell
25	chr2:39742200-39744800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:39742200-39744800	Enhancers	Right Ventricle	heart
27	chr2:39742400-39744600	Enhancers	Fetal Kidney	kidney
28	chr2:39742400-39744800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr2:39742400-39744800	Enhancers	Fetal Intestine Large	intestine
30	chr2:39742400-39745200	Enhancers	Fetal Stomach	stomach
31	chr2:39742400-39745600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr2:39742600-39744000	Enhancers	Fetal Muscle Trunk	muscle
33	chr2:39742600-39744200	Enhancers	H1 Cell Line	embryonic stem cell
34	chr2:39742600-39744200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:39742600-39744200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:39742600-39744200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:39742600-39744200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:39742600-39744600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:39742600-39744600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr2:39742600-39744600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr2:39742600-39745000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:39742600-39745000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:39742600-39745000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:39742600-39745400	Enhancers	Rectal Smooth Muscle	rectum
45	chr2:39742800-39744800	Enhancers	HSMMtube	muscle
46	chr2:39742800-39745600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:39742800-39745600	Enhancers	A549	lung
48	chr2:39742800-39746200	Enhancers	Colon Smooth Muscle	Colon
49	chr2:39742800-39746800	Weak transcription	Primary B cells from cord blood	blood
50	chr2:39743000-39744200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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