Variant report

Variant	rs2240323
Chromosome Location	chr12:120600172-120600173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120598920-120601146	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:120599139-120601290	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:120599342-120601349	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr12:120598663-120601231	K562	blood:	n/a	n/a
5	ESR1	chr12:120599989-120600337	T-47D	breast:	n/a	n/a
6	ESR1	chr12:120599987-120600323	T-47D	breast:	n/a	n/a
7	POLR2A	chr12:120598661-120601123	K562	blood:	n/a	n/a
8	POLR2A	chr12:120598718-120601344	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:120599314-120600708	K562	blood:	n/a	n/a
10	POLR2A	chr12:120596887-120601806	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:120599525-120601063	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:120598391-120601453	K562	blood:	n/a	n/a
13	POLR2A	chr12:120598707-120600356	K562	blood:	n/a	n/a
14	POLR2A	chr12:120599065-120601439	GM12891	blood:	n/a	n/a
15	POLR2A	chr12:120599027-120601308	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:120598620-120601318	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:120598821-120600210	GM12878	blood:	n/a	n/a
18	ESR1	chr12:120600010-120600412	T-47D	breast:	n/a	n/a
19	POLR2A	chr12:120598769-120601135	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:120598262-120601509	GM12892	blood:	n/a	n/a
21	ESR1	chr12:120600005-120600342	T-47D	breast:	n/a	n/a
22	POLR2A	chr12:120599129-120601067	K562	blood:	n/a	n/a
23	POLR2A	chr12:120600067-120600566	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:120599797-120600815	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr12:120599729-120601082	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:120598746-120601231	GM12892	blood:	n/a	n/a
27	POLR2A	chr12:120599563-120600281	HL-60	blood:	n/a	n/a
28	POLR2A	chr12:120598504-120601234	A549	lung:	n/a	n/a
29	POLR2A	chr12:120599568-120600223	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:120599408-120600617	GM12892	blood:	n/a	n/a
31	POLR2A	chr12:120599666-120600206	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:120597159..120601536-chr12:120728330..120731002,4	MCF-7	breast:
2	chr12:120599855..120602447-chr12:120604599..120606959,2	MCF-7	breast:
3	chr12:120600039..120601830-chr12:120632774..120634294,2	MCF-7	breast:
4	chr12:120598911..120601792-chr12:120728413..120730784,2	MCF-7	breast:

No data

Variant related genes	Relation type
GCN1L1	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000089154	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10437836	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10744748	0.82[JPT][hapmap]
rs11065035	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1151824	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1151825	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1151827	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1151832	0.91[JPT][hapmap]
rs1151837	0.90[JPT][hapmap]
rs11833158	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11836049	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1183781	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs12305184	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12306075	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12310433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12312562	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12320253	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12578300	0.90[EUR][1000 genomes]
rs1634814	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2074540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2238155	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2240312	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs2240314	0.86[EUR][1000 genomes]
rs2240315	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2240317	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2240318	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240319	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240320	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240324	0.90[ASN][1000 genomes]
rs2240325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2269940	1.00[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs2269941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269943	0.91[EUR][1000 genomes]
rs2269944	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283362	1.00[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2283364	0.95[JPT][hapmap]
rs2286043	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286044	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2286045	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2422	0.86[JPT][hapmap]
rs3742039	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs3815210	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3888586	0.95[JPT][hapmap]
rs4522230	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57546423	0.87[EUR][1000 genomes]
rs57780521	0.85[EUR][1000 genomes]
rs59601514	0.95[EUR][1000 genomes]
rs60271600	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7133235	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7134706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7135914	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7294892	0.86[EUR][1000 genomes]
rs7296380	0.94[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs7299429	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7301660	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7953741	0.86[EUR][1000 genomes]
rs7978061	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7978175	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9630281	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9651914	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2240323	GCN1L1	cis	Lymphoblastoid	GTEx
rs2240323	GCN1L1	cis	multi-tissue	Pritchard
rs2240323	FBXO21	cis	parietal	SCAN
rs2240323	SETD1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120563000-120605600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:120563000-120629800	Strong transcription	Fetal Stomach	stomach
3	chr12:120563000-120630200	Strong transcription	Fetal Muscle Leg	muscle
4	chr12:120563200-120602800	Strong transcription	Brain Germinal Matrix	brain
5	chr12:120563200-120630400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:120563400-120616200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:120563400-120629200	Strong transcription	Fetal Intestine Small	intestine
8	chr12:120563400-120630200	Strong transcription	Fetal Thymus	thymus
9	chr12:120563600-120602400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:120563600-120603600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:120563600-120603800	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:120563600-120605600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:120563600-120626000	Strong transcription	Brain Cingulate Gyrus	brain
14	chr12:120563600-120626200	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr12:120563600-120629000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:120563600-120630200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:120563600-120630200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:120563600-120630200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:120563600-120630200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:120563600-120630200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:120563800-120602600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:120563800-120602600	Strong transcription	Primary T cells from cord blood	blood
23	chr12:120563800-120602600	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr12:120563800-120602800	Strong transcription	Dnd41	blood
25	chr12:120563800-120603600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:120563800-120629800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:120563800-120630000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:120563800-120630200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:120564000-120603600	Strong transcription	Brain Angular Gyrus	brain
30	chr12:120564000-120603800	Strong transcription	Thymus	Thymus
31	chr12:120564200-120624400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:120564200-120629600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:120564400-120602600	Strong transcription	Brain Hippocampus Middle	brain
34	chr12:120564400-120602600	Strong transcription	Placenta	Placenta
35	chr12:120564400-120602600	Strong transcription	HSMMtube	muscle
36	chr12:120564400-120603600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:120564400-120603600	Strong transcription	Rectal Smooth Muscle	rectum
38	chr12:120564400-120603600	Strong transcription	Right Ventricle	heart
39	chr12:120564400-120628600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:120564400-120631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:120564600-120602800	Strong transcription	Ovary	ovary
42	chr12:120564600-120603800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:120564600-120603800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr12:120564800-120618000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:120565000-120602600	Strong transcription	Aorta	Aorta
46	chr12:120565000-120603400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:120565000-120628800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:120565000-120630200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:120565000-120630800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:120565200-120602400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links