Variant report

Variant	rs1165681
Chromosome Location	chr12:104325111-104325112
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	RCOR1	chr12:104323737-104325674	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:104325096-104325540	U87	brain:	n/a	n/a
3	RUNX3	chr12:104321971-104325533	GM12878	blood:	n/a	n/a
4	CHD2	chr12:104323166-104325167	Hela-S3	cervix:	n/a	chr12:104324650-104324660
5	POLR2A	chr12:104322428-104325591	SK-N-MC	brain:	n/a	n/a
6	WRNIP1	chr12:104322092-104325599	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:104322498-104325320	GM12878	blood:	n/a	n/a
8	MAX	chr12:104322072-104325169	GM12878	blood:	n/a	chr12:104324136-104324146 chr12:104322562-104322569 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104322561-104322572 chr12:104324369-104324379
9	MXI1	chr12:104323090-104325397	Hela-S3	cervix:	n/a	chr12:104323780-104323795 chr12:104323778-104323793
10	MYC	chr12:104323016-104325167	K562	blood:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
11	RELA	chr12:104321990-104325291	GM19193	blood:	n/a	n/a
12	MAX	chr12:104324614-104325123	K562	blood:	n/a	chr12:104324993-104325000 chr12:104324642-104324652
13	MAX	chr12:104322913-104325128	Hela-S3	cervix:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
14	MAX	chr12:104322651-104325593	A549	lung:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
15	CREB1	chr12:104322814-104325148	HepG2	liver:	n/a	n/a
16	E2F6	chr12:104322797-104325182	K562	blood:	n/a	chr12:104324137-104324146 chr12:104324434-104324444 chr12:104323616-104323625 chr12:104323708-104323719
17	POLR2A	chr12:104323967-104325720	GM12891	blood:	n/a	n/a
18	TEAD4	chr12:104322407-104327510	K562	blood:	n/a	n/a
19	POLR2A	chr12:104323946-104325121	K562	blood:	n/a	n/a
20	POLR2A	chr12:104323006-104326144	IMR90	lung:	n/a	n/a
21	MYC	chr12:104322667-104325237	K562	blood:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
22	MYC	chr12:104322219-104325211	NB4	blood:	n/a	chr12:104324136-104324146 chr12:104322562-104322569 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104322561-104322572 chr12:104324369-104324379
23	MTA3	chr12:104321890-104325504	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:104323974-104325332	Hela-S3	cervix:	n/a	n/a
25	RFX5	chr12:104322611-104325806	SK-N-SH	brain:	n/a	chr12:104323780-104323789 chr12:104323777-104323791 chr12:104323779-104323794 chr12:104323779-104323794 chr12:104323779-104323794 chr12:104323778-104323795
26	POLR2A	chr12:104324627-104325462	HepG2	liver:	n/a	n/a
27	SIN3A	chr12:104322361-104325276	GM12878	blood:	n/a	chr12:104324624-104324633 chr12:104323584-104323593 chr12:104324039-104324047
28	MAX	chr12:104322765-104325318	A549	lung:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
29	POLR2A	chr12:104324024-104325565	K562	blood:	n/a	n/a
30	POLR2A	chr12:104323979-104325538	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr12:104322849-104325508	Hela-S3	cervix:	n/a	n/a
32	MAX	chr12:104323579-104325313	MCF-7	breast:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
33	MYC	chr12:104324852-104325334	H1-hESC	embryonic stem cell:	n/a	chr12:104324993-104325000
34	MYC	chr12:104322401-104325286	K562	blood:	n/a	chr12:104324136-104324146 chr12:104322562-104322569 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104322561-104322572 chr12:104324369-104324379
35	POLR2A	chr12:104323989-104328526	K562	blood:	n/a	n/a
36	POLR2A	chr12:104323632-104325579	GM12892	blood:	n/a	n/a
37	POLR2A	chr12:104322439-104326717	MCF10A-Er-Src	breast:	n/a	n/a
38	MAX	chr12:104324705-104325114	HepG2	liver:	n/a	chr12:104324993-104325000
39	POLR2A	chr12:104323645-104325618	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr12:104322500-104325152	H1-hESC	embryonic stem cell:	n/a	chr12:104323780-104323795 chr12:104323778-104323793
41	POLR2A	chr12:104322871-104325325	Raji	blood:	n/a	n/a
42	POLR2A	chr12:104323715-104325143	Hela-S3	cervix:	n/a	n/a
43	RAD21	chr12:104324666-104325331	IMR90	lung:	n/a	chr12:104324761-104324774
44	PML	chr12:104323762-104328552	K562	blood:	n/a	n/a
45	POLR2A	chr12:104322548-104325574	PBDE	blood:	n/a	n/a
46	MAX	chr12:104322474-104325199	K562	blood:	n/a	chr12:104324136-104324146 chr12:104322562-104322569 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104322561-104322572 chr12:104324369-104324379
47	SIX5	chr12:104322786-104325275	A549	lung:	n/a	chr12:104323586-104323595 chr12:104323588-104323597 chr12:104323585-104323599
48	PML	chr12:104321903-104325251	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:104323674-104325727	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr12:104321755-104325879	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104298858..104303101-chr12:104321689..104325332,4	K562	blood:
2	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:
3	chr12:104233909..104239694-chr12:104322835..104327398,8	K562	blood:
4	chr12:104233715..104236918-chr12:104321893..104325386,6	K562	blood:
5	chr12:104319631..104321504-chr12:104324248..104326474,2	MCF-7	breast:
6	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
7	chr12:104322684..104325586-chr12:104530441..104532019,2	K562	blood:
8	chr12:104276117..104279238-chr12:104322705..104326968,4	K562	blood:
9	chr12:104322943..104325215-chr12:104358408..104360868,4	MCF-7	breast:
10	chr1:46152208..46153875-chr12:104323647..104326577,2	K562	blood:
11	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214198	TF binding region
ENSG00000159596	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000214198	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10735390	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1370410	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs1370776	0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs1866069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576942	0.80[YRI][hapmap]
rs2583223	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583283	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2722176	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1165681	TU12B1-TY	cis	multi-tissue	Pritchard
rs1165681	TCP11L2	cis	cerebellum	SCAN
rs1165681	ACTR6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104322000-104325200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr12:104322000-104325200	Active TSS	Rectal Smooth Muscle	rectum
3	chr12:104322200-104325200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:104322200-104325200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:104322200-104326200	Active TSS	H1 Cell Line	embryonic stem cell
6	chr12:104322200-104326200	Active TSS	GM12878-XiMat	blood
7	chr12:104322400-104325200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:104322400-104325200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr12:104322400-104325200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr12:104322400-104325400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:104322400-104325600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:104322400-104325800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr12:104322400-104326000	Active TSS	Colonic Mucosa	Colon
14	chr12:104322400-104326000	Active TSS	Fetal Intestine Small	intestine
15	chr12:104322400-104327000	Active TSS	Right Atrium	heart
16	chr12:104322600-104325200	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr12:104322600-104325200	Active TSS	Brain Substantia Nigra	brain
18	chr12:104322600-104325400	Active TSS	Brain Hippocampus Middle	brain
19	chr12:104322600-104325400	Active TSS	Gastric	stomach
20	chr12:104322600-104325400	Active TSS	Placenta Amnion	Placenta Amnion
21	chr12:104322600-104325600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:104322600-104325600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:104322600-104325600	Active TSS	Esophagus	oesophagus
24	chr12:104322600-104325600	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr12:104322600-104325800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:104322600-104325800	Active TSS	Fetal Muscle Trunk	muscle
27	chr12:104322600-104326400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:104322600-104327000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:104322600-104327200	Active TSS	Aorta	Aorta
30	chr12:104322800-104325200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:104322800-104325200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:104322800-104325200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:104322800-104325200	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:104322800-104325200	Active TSS	Fetal Brain Female	brain
35	chr12:104322800-104325200	Active TSS	Spleen	Spleen
36	chr12:104322800-104325400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:104322800-104325400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:104322800-104325400	Active TSS	Fetal Kidney	kidney
39	chr12:104322800-104325400	Active TSS	Stomach Mucosa	stomach
40	chr12:104322800-104325400	Bivalent/Poised TSS	HepG2	liver
41	chr12:104322800-104325600	Active TSS	Left Ventricle	heart
42	chr12:104322800-104325600	Active TSS	Lung	lung
43	chr12:104322800-104325600	Active TSS	Small Intestine	intestine
44	chr12:104322800-104326000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:104322800-104326000	Active TSS	Fetal Intestine Large	intestine
46	chr12:104322800-104326000	Active TSS	NHDF-Ad	bronchial
47	chr12:104322800-104326200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:104322800-104326200	Active TSS	Fetal Stomach	stomach
49	chr12:104322800-104326200	Active TSS	Ovary	ovary
50	chr12:104322800-104326600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links