Variant report

Variant	rs2277324
Chromosome Location	chr12:58013175-58013176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr12:58012931-58014255	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr12:58012720-58016103	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr12:58013091-58013850	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3A	chr12:58013111-58013759	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr12:58013099-58013878	HepG2	liver:	n/a	n/a
6	CHD2	chr12:58013094-58013419	HepG2	liver:	n/a	n/a
7	CHD2	chr12:58013165-58013357	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58013172-58013222	ProgFib	skin:	n/a
2	chr12:58013174-58013224	Hela-S3	cervix:	n/a
3	chr12:58013174-58013224	HCM	heart:	n/a
4	chr12:58013174-58013224	SK-N-SH	brain:	n/a
5	chr12:58013174-58013224	NH-A	brain:	n/a
6	chr12:58013174-58013224	AoSMC	blood vessel:	n/a
7	chr12:58013172-58013222	SK-N-SH	brain:	n/a
8	chr12:58013172-58013222	HRPEpiC	eye:	n/a
9	chr12:58013174-58013224	HUVEC	blood vessel:	n/a
10	chr12:58013174-58013224	NB4	blood:	n/a
11	chr12:58013174-58013224	NHDF-neo	bronchial:	n/a
12	chr12:58013172-58013222	HCT-116	colon:	n/a
13	chr12:58013172-58013222	PANC-1	pancreas:	n/a
14	chr12:58013174-58013224	AG04449	skin:	fetal
15	chr12:58013172-58013222	HEEpiC	esophagus:	n/a
16	chr12:58013174-58013224	Jurkat	blood:	n/a
17	chr12:58013172-58013222	HNPCEpiC	eye:	n/a
18	chr12:58013174-58013224	HRE	kidney:	n/a
19	chr12:58013174-58013224	HL-60	blood:	n/a
20	chr12:58013172-58013222	MCF10A-Er-Src	breast:	n/a
21	chr12:58013174-58013224	GM06990	blood:	n/a
22	chr12:58013172-58013222	Caco-2	colon:	n/a
23	chr12:58013174-58013224	H1-hESC	embryonic stem cell:	embryo
24	chr12:58013174-58013224	CMK	blood:	n/a
25	chr12:58013174-58013224	HCT-116	colon:	n/a
26	chr12:58013172-58013222	U87	brain:	n/a
27	chr12:58013174-58013224	GM12892	blood:	n/a
28	chr12:58013172-58013222	AG04449	skin:	fetal
29	chr12:58013172-58013222	SKMC	muscle:	n/a
30	chr12:58013172-58013222	HL-60	blood:	n/a
31	chr12:58013174-58013224	HIPEpiC	eye:	n/a
32	chr12:58013172-58013222	GM19239	blood:	n/a
33	chr12:58013172-58013222	RPTEC	kidney:	n/a
34	chr12:58013174-58013224	T-47D	breast:	n/a
35	chr12:58013172-58013222	HAEpiC	amniotic membrane:	n/a
36	chr12:58013172-58013222	HMEC	breast:	n/a
37	chr12:58013174-58013224	HepG2	liver:	n/a
38	chr12:58013172-58013222	HEK293	kidney:	embryo
39	chr12:58013174-58013224	HNPCEpiC	eye:	n/a
40	chr12:58013172-58013222	ovcar-3	ovarian:	n/a
41	chr12:58013174-58013224	ProgFib	skin:	n/a
42	chr12:58013174-58013224	SAEC	small airway:	n/a
43	chr12:58013174-58013224	GM12891	blood:	n/a
44	chr12:58013172-58013222	GM06990	blood:	n/a
45	chr12:58013172-58013222	CMK	blood:	n/a
46	chr12:58013174-58013224	NHBE	bronchial:	n/a
47	chr12:58013172-58013222	MCF-7	breast:	n/a
48	chr12:58013172-58013222	NHBE	bronchial:	n/a
49	chr12:58013172-58013222	GM12892	blood:	n/a
50	chr12:58013172-58013222	SK-N-MC	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57913091..57915646-chr12:58010883..58013272,4	K562	blood:
2	chr12:58013150..58015350-chr12:58146267..58147778,2	K562	blood:

No data

Variant related genes	Relation type
SLC26A10	TF binding region
ENSG00000224713	TF binding region
ENSG00000224713	CpG island
SLC26A10	CpG island
ENSG00000135446	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1027315	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1038914	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1050045	0.90[JPT][hapmap]
rs12368653	0.81[MEX][hapmap]
rs1552842	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1564374	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1873919	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307095	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2640610	0.88[ASN][1000 genomes]
rs34271193	0.83[ASN][1000 genomes]
rs6581147	0.82[ASN][1000 genomes]
rs7134861	0.84[ASN][1000 genomes]
rs7295422	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs7304145	0.92[ASN][1000 genomes]
rs7311632	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs7966795	0.88[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs799265	0.90[JPT][hapmap]
rs903067	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs923828	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers 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	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2277324	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs2277324	FAM119B	cis	cerebellum	SCAN
rs2277324	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs2277324	TSPAN31	cis	cerebellum	SCAN
rs2277324	NCKAP1L	cis	parietal	SCAN
rs2277324	FAM119B	cis	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58005600-58013200	Weak transcription	Gastric	stomach
2	chr12:58006200-58014800	Weak transcription	Brain Angular Gyrus	brain
3	chr12:58006600-58013200	Weak transcription	Pancreas	Pancrea
4	chr12:58010200-58013600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:58010400-58013600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr12:58010400-58014000	Weak transcription	Brain Substantia Nigra	brain
7	chr12:58010400-58014400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:58010600-58014000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:58010600-58014000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:58010600-58014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:58010800-58013200	Weak transcription	Esophagus	oesophagus
12	chr12:58010800-58013600	Weak transcription	Brain Anterior Caudate	brain
13	chr12:58011400-58014600	Weak transcription	Ovary	ovary
14	chr12:58011600-58013400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:58011600-58018000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:58011800-58013200	Weak transcription	Left Ventricle	heart
17	chr12:58011800-58013200	Weak transcription	Right Atrium	heart
18	chr12:58011800-58014200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:58011800-58015000	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:58011800-58018800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:58012000-58013200	Weak transcription	Spleen	Spleen
22	chr12:58012000-58015000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:58012000-58015000	Weak transcription	K562	blood
24	chr12:58012000-58019000	Weak transcription	Aorta	Aorta
25	chr12:58012600-58013600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:58012600-58014600	Bivalent Enhancer	Primary B cells from cord blood	blood
27	chr12:58012800-58013200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:58012800-58013200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:58012800-58013800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr12:58012800-58014400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr12:58012800-58014800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:58013000-58013200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr12:58013000-58013200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:58013000-58013200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr12:58013000-58013200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:58013000-58013200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:58013000-58013200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:58013000-58013200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:58013000-58013200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:58013000-58013200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
41	chr12:58013000-58013400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
42	chr12:58013000-58013400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
43	chr12:58013000-58013400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:58013000-58013400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
45	chr12:58013000-58013600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:58013000-58013600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr12:58013000-58013800	Bivalent Enhancer	Fetal Thymus	thymus
48	chr12:58013000-58013800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
49	chr12:58013000-58014000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
50	chr12:58013000-58014000	Flanking Bivalent TSS/Enh	HepG2	liver

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