Variant report

Variant	rs3136228
Chromosome Location	chr2:48009816-48009817
allele	G/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	TBP	chr2:48009724-48011312	H1-hESC	embryonic stem cell:	n/a	n/a
2	EGR1	chr2:48009760-48010441	ECC-1	luminal epithelium:	n/a	chr2:48009933-48009946 chr2:48010088-48010102 chr2:48010099-48010109
3	GABPA	chr2:48009709-48010568	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:48009717-48010552	SK-N-SH	brain:	n/a	n/a
5	SIN3AK20	chr2:48009451-48011776	MCF-7	breast:	n/a	n/a
6	SMC3	chr2:48009518-48010524	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr2:48009607-48009851	HepG2	liver:	n/a	n/a
8	MAX	chr2:48009528-48011580	NB4	blood:	n/a	chr2:48011032-48011042
9	POLR2A	chr2:48009627-48011001	HL-60	blood:	n/a	n/a
10	CCNT2	chr2:48009723-48011419	K562	blood:	n/a	chr2:48011044-48011053 chr2:48010131-48010140 chr2:48010643-48010652 chr2:48010993-48011002 chr2:48010712-48010721
11	POLR2A	chr2:48009642-48010925	U87	brain:	n/a	n/a
12	POLR2A	chr2:48009488-48011430	HepG2	liver:	n/a	n/a
13	JUND	chr2:48009510-48010538	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAFK	chr2:48009618-48009842	HepG2	liver:	n/a	chr2:48009779-48009793 chr2:48009780-48009796 chr2:48009781-48009792 chr2:48009781-48009792
15	FOXM1	chr2:48009670-48010610	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:48009786-48010504	GM10847	blood:	n/a	n/a
17	POLR2A	chr2:48009672-48010122	H1-hESC	embryonic stem cell:	n/a	n/a
18	MBD4	chr2:48009392-48009994	HepG2	liver:	n/a	n/a
19	SPI1	chr2:48009730-48010392	GM12878	blood:	n/a	chr2:48009943-48009956
20	MAX	chr2:48009727-48010893	HepG2	liver:	n/a	n/a
21	REST	chr2:48009658-48010636	HepG2	liver:	n/a	chr2:48010029-48010042
22	STAT5A	chr2:48009734-48010637	GM12878	blood:	n/a	chr2:48010158-48010170
23	SPI1	chr2:48009747-48010123	GM12878	blood:	n/a	chr2:48009943-48009956
24	BHLHE40	chr2:48009535-48010884	K562	blood:	n/a	n/a
25	SPI1	chr2:48009764-48010338	GM12891	blood:	n/a	chr2:48009943-48009956
26	POLR2A	chr2:48009717-48010617	ECC-1	luminal epithelium:	n/a	n/a
27	CHD2	chr2:48009671-48010970	HepG2	liver:	n/a	chr2:48010273-48010283
28	GABPA	chr2:48009784-48010075	HepG2	liver:	n/a	n/a
29	SP1	chr2:48009715-48010611	H1-hESC	embryonic stem cell:	n/a	chr2:48010130-48010140 chr2:48010157-48010166 chr2:48010129-48010141 chr2:48009881-48009888 chr2:48010129-48010140 chr2:48010130-48010140 chr2:48010156-48010167 chr2:48010156-48010168 chr2:48010156-48010168 chr2:48010130-48010139 chr2:48010130-48010139 chr2:48010131-48010140 chr2:48010157-48010171 chr2:48010046-48010060 chr2:48010129-48010141 chr2:48010130-48010144 chr2:48010224-48010245 chr2:48010187-48010198
30	MYC	chr2:48009537-48011035	A549	lung:	n/a	n/a
31	POLR2A	chr2:48009321-48010999	Hela-S3	cervix:	n/a	n/a
32	EP300	chr2:48009619-48010969	ECC-1	luminal epithelium:	n/a	n/a
33	BCLAF1	chr2:48009585-48010673	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:48009656-48010632	PBDE	blood:	n/a	n/a
35	EGR1	chr2:48009791-48010060	GM12878	blood:	n/a	chr2:48009933-48009946
36	POLR2A	chr2:48009627-48011455	K562	blood:	n/a	n/a
37	TAF1	chr2:48009724-48010142	A549	lung:	n/a	n/a
38	E2F6	chr2:48009686-48011751	A549	lung:	n/a	chr2:48010286-48010295 chr2:48011052-48011064 chr2:48010287-48010294 chr2:48010235-48010244 chr2:48010287-48010294 chr2:48009932-48009941 chr2:48011044-48011053 chr2:48010285-48010296 chr2:48010286-48010294 chr2:48010750-48010759 chr2:48010286-48010298 chr2:48010287-48010294 chr2:48011131-48011140
39	POLR2A	chr2:48009732-48010644	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr2:48009691-48011296	GM18526	blood:	n/a	n/a
41	RELA	chr2:48009631-48010639	GM12891	blood:	n/a	n/a
42	MAX	chr2:48009393-48010957	Hela-S3	cervix:	n/a	n/a
43	EGR1	chr2:48009700-48010541	MCF-7	breast:	n/a	chr2:48009933-48009946 chr2:48010088-48010102 chr2:48010099-48010109
44	POLR2A	chr2:48009667-48011276	HepG2	liver:	n/a	n/a
45	ZKSCAN1	chr2:48009499-48010537	Hela-S3	cervix:	n/a	n/a
46	MAX	chr2:48009757-48011049	H1-hESC	embryonic stem cell:	n/a	chr2:48011032-48011042
47	POLR2A	chr2:48009704-48011601	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr2:48009620-48011271	GM18505	blood:	n/a	n/a
49	POLR2A	chr2:48009647-48011413	K562	blood:	n/a	n/a
50	MAX	chr2:48009771-48011556	K562	blood:	n/a	chr2:48011032-48011042

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:48009809-48009859	HRCEpiC	kidney:	n/a
2	chr2:48009809-48009859	AG10803	skin:	n/a
3	chr2:48009809-48009859	U87	brain:	n/a
4	chr2:48009809-48009859	PrEC	prostate:	n/a
5	chr2:48009809-48009859	GM19239	blood:	n/a
6	chr2:48009809-48009859	H1-hESC	embryonic stem cell:	embryo
7	chr2:48009809-48009859	ovcar-3	ovarian:	n/a
8	chr2:48009809-48009859	Hela-S3	cervix:	n/a
9	chr2:48009809-48009859	AoSMC	blood vessel:	n/a
10	chr2:48009809-48009859	HNPCEpiC	eye:	n/a
11	chr2:48009809-48009859	AG04450	lung:	fetal
12	chr2:48009809-48009859	HIPEpiC	eye:	n/a
13	chr2:48009809-48009859	GM12878	blood:	n/a
14	chr2:48009809-48009859	ProgFib	skin:	n/a
15	chr2:48009809-48009859	BJ	skin:	n/a
16	chr2:48009809-48009859	HPAEpiC	pulmonary alveolar:	n/a
17	chr2:48009809-48009859	HCM	heart:	n/a
18	chr2:48009809-48009859	T-47D	breast:	n/a
19	chr2:48009809-48009859	HCT-116	colon:	n/a
20	chr2:48009809-48009859	HEEpiC	esophagus:	n/a
21	chr2:48009809-48009859	IMR90	lung:	fetal
22	chr2:48009809-48009859	HCPEpiC	choroid plexus:	n/a
23	chr2:48009809-48009859	AG04449	skin:	fetal
24	chr2:48009809-48009859	CMK	blood:	n/a
25	chr2:48009809-48009859	HL-60	blood:	n/a
26	chr2:48009809-48009859	HCF	heart:	n/a
27	chr2:48009809-48009859	MCF10A-Er-Src	breast:	n/a
28	chr2:48009809-48009859	SK-N-SH_RA	brain:	n/a
29	chr2:48009809-48009859	SKMC	muscle:	n/a
30	chr2:48009809-48009859	NB4	blood:	n/a
31	chr2:48009809-48009859	HUVEC	blood vessel:	n/a
32	chr2:48009809-48009859	LNCaP	prostate:	n/a
33	chr2:48009809-48009859	GM12891	blood:	n/a
34	chr2:48009809-48009859	AG09319	gingival:	n/a
35	chr2:48009809-48009859	HRPEpiC	eye:	n/a
36	chr2:48009809-48009859	AG09309	skin:	n/a
37	chr2:48009809-48009859	HepG2	liver:	n/a
38	chr2:48009809-48009859	BE2_C	brain:	n/a
39	chr2:48009809-48009859	Jurkat	blood:	n/a
40	chr2:48009809-48009859	HAEpiC	amniotic membrane:	n/a
41	chr2:48009809-48009859	MCF-7	breast:	n/a
42	chr2:48009809-48009859	GM06990	blood:	n/a
43	chr2:48009809-48009859	Caco-2	colon:	n/a
44	chr2:48009809-48009859	NHDF-neo	bronchial:	n/a
45	chr2:48009809-48009859	SK-N-MC	brain:	n/a
46	chr2:48009809-48009859	HMEC	breast:	n/a
47	chr2:48009809-48009859	A549	lung:	n/a
48	chr2:48009809-48009859	PFSK-1	brain:	n/a
49	chr2:48009809-48009859	SAEC	small airway:	n/a
50	chr2:48009809-48009859	HRE	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:62501791..62502687-chr2:48009810..48010670,2	Hela-S3	cervix:
2	chr2:48008927..48012318-chr2:48131369..48134669,5	MCF-7	breast:
3	chr10:70091529..70092348-chr2:48009738..48010379,2	Hela-S3	cervix:
4	chr2:47629900..47631449-chr2:48009384..48011204,2	K562	blood:
5	chr16:27279521..27280140-chr2:48009595..48010496,2	Hela-S3	cervix:
6	chr2:48009680..48011593-chr2:48034365..48037361,4	K562	blood:
7	chr2:48008730..48016091-chr2:48023378..48031018,13	K562	blood:
8	chr2:48009330..48011315-chr2:48667151..48669363,2	MCF-7	breast:
9	chr1:17231455..17232098-chr2:48009621..48010207,2	Hela-S3	cervix:
10	chr2:47400478..47403818-chr2:48008752..48011597,4	K562	blood:
11	chr2:48009081..48011260-chr2:48666512..48669305,2	K562	blood:
12	chr2:48009241..48011521-chr2:48133698..48136009,2	K562	blood:
13	chr2:48009564..48012056-chr2:48131613..48133953,3	MCF-7	breast:

Variant related genes	Relation type
MSH6	TF binding region
MSH6	CpG island
ENSG00000143933	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000138081	Chromatin interaction
ENSG00000169189	Chromatin interaction
ENSG00000245888	Chromatin interaction
ENSG00000095002	Chromatin interaction
ENSG00000235369	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000096746	Chromatin interaction
ENSG00000162869	Chromatin interaction
ENSG00000233230	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10490302	0.91[LWK][hapmap];0.86[MEX][hapmap];0.95[YRI][hapmap]
rs1800935	0.85[MEX][hapmap];0.83[MKK][hapmap];0.82[AMR][1000 genomes]
rs3136250	0.84[AMR][1000 genomes]
rs3136262	0.83[AMR][1000 genomes]
rs3136267	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136272	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136292	0.80[AMR][1000 genomes]
rs759050	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]

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	nsv873999	chr2:47916074-48019485	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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	36 gene(s)	inside rSNPs	diseases
4	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv3392564	chr2:48009598-48012596	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3136228	FOXN2	cis	cerebellum	SCAN
rs3136228	MSH6	cis	parietal	SCAN
rs3136228	PLEKHH2	cis	parietal	SCAN
rs3136228	FOXN2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48008400-48011400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr2:48009000-48011400	Active TSS	Rectal Smooth Muscle	rectum
3	chr2:48009000-48012400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:48009200-48010000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:48009200-48012000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:48009200-48012200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:48009200-48012400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:48009200-48012600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr2:48009200-48012800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr2:48009200-48012800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr2:48009400-48010000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr2:48009400-48010000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr2:48009400-48010000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr2:48009400-48010000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:48009400-48010000	Flanking Active TSS	Dnd41	blood
16	chr2:48009400-48010000	Flanking Active TSS	HMEC	breast
17	chr2:48009400-48010000	Flanking Active TSS	HUVEC	blood vessel
18	chr2:48009400-48010000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr2:48009400-48010600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr2:48009400-48011000	Bivalent/Poised TSS	HepG2	liver
21	chr2:48009400-48011400	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr2:48009400-48011400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:48009400-48011400	Active TSS	Stomach Smooth Muscle	stomach
24	chr2:48009400-48011600	Active TSS	Brain Anterior Caudate	brain
25	chr2:48009400-48011600	Active TSS	Brain Substantia Nigra	brain
26	chr2:48009400-48011600	Active TSS	Left Ventricle	heart
27	chr2:48009400-48011600	Active TSS	Pancreas	Pancrea
28	chr2:48009400-48011600	Active TSS	Psoas Muscle	Psoas
29	chr2:48009400-48011600	Active TSS	Right Ventricle	heart
30	chr2:48009400-48011600	Active TSS	Stomach Mucosa	stomach
31	chr2:48009400-48011600	Active TSS	NHEK	skin
32	chr2:48009400-48011800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:48009400-48011800	Active TSS	Brain Germinal Matrix	brain
34	chr2:48009400-48011800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:48009400-48011800	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr2:48009400-48011800	Active TSS	Fetal Brain Female	brain
37	chr2:48009400-48011800	Active TSS	Fetal Lung	lung
38	chr2:48009400-48011800	Active TSS	Fetal Stomach	stomach
39	chr2:48009400-48011800	Active TSS	A549	lung
40	chr2:48009400-48012000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:48009400-48012000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:48009400-48012000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:48009400-48012000	Active TSS	Brain Angular Gyrus	brain
44	chr2:48009400-48012000	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr2:48009400-48012000	Active TSS	Right Atrium	heart
46	chr2:48009400-48012000	Active TSS	NHDF-Ad	bronchial
47	chr2:48009400-48012200	Active TSS	H9 Cell Line	embryonic stem cell
48	chr2:48009400-48012200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr2:48009400-48012200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr2:48009400-48012200	Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links