Variant report

Variant	rs3812803
Chromosome Location	chr12:104200460-104200461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr12:104200451-104201135	SK-N-SH	brain:	n/a	n/a
2	SPI1	chr12:104200413-104200987	HL-60	blood:	n/a	chr12:104200581-104200590
3	NFIC	chr12:104200358-104201198	SK-N-SH	brain:	n/a	n/a
4	JUND	chr12:104200421-104201200	SK-N-SH	brain:	n/a	n/a
5	FOXM1	chr12:104200378-104201320	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr12:104200404-104201158	SK-N-SH	brain:	n/a	n/a
7	EP300	chr12:104200447-104201248	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr12:104200415-104201210	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr12:104200280-104201271	SK-N-SH	brain:	n/a	chr12:104201098-104201109 chr12:104201096-104201105
10	TCF12	chr12:104200330-104201341	SK-N-SH	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104192165..104193945-chr12:104199242..104201108,2	K562	blood:
2	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:
3	chr12:104199856..104205672-chr12:104232098..104237727,8	K562	blood:
4	chr12:104198469..104201339-chr12:104203097..104205273,3	MCF-7	breast:
5	chr12:104198690..104201561-chr12:104203107..104206456,4	K562	blood:
6	chr12:104200257..104201924-chr12:104226182..104228413,2	K562	blood:
7	chr12:104198918..104202818-chr12:104225755..104230550,5	K562	blood:
8	chr12:104198690..104200506-chr12:104204020..104206335,2	K562	blood:
9	chr12:104196315..104200600-chr12:104233023..104235965,5	MCF-7	breast:
10	chr12:104199289..104201376-chr12:104228152..104230435,2	MCF-7	breast:

No data

Variant related genes	Relation type
NT5DC3	TF binding region
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10861094	0.91[JPT][hapmap]
rs10861104	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10861105	0.95[CHB][hapmap];0.96[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861109	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111779	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs11111786	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11111788	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11111789	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11111791	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11111792	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111793	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11111795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111796	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12228207	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12229276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866295	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34307072	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35371470	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35746861	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35945096	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36034617	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3935416	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964289	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964623	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964780	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4964794	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964805	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964806	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964812	0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67825151	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7134701	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs934847	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3812803	RP11-341G23.4	cis	Artery Tibial	GTEx
rs3812803	RP11-341G23.4	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:104187400-104206800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
7	chr12:104190800-104201800	Weak transcription	Gastric	stomach
8	chr12:104190800-104204400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:104192600-104206600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:104193600-104204000	Weak transcription	Primary T cells from cord blood	blood
14	chr12:104194000-104206800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:104194400-104207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:104194600-104203800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:104194600-104207000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:104194600-104214600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:104194600-104214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:104194800-104207200	Weak transcription	Adipose Nuclei	Adipose
21	chr12:104194800-104215200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:104195000-104200800	Weak transcription	Spleen	Spleen
23	chr12:104195000-104201800	Weak transcription	Stomach Mucosa	stomach
24	chr12:104195000-104203600	Weak transcription	Fetal Intestine Large	intestine
25	chr12:104195000-104204400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:104195000-104205200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:104195000-104207800	Weak transcription	Fetal Lung	lung
28	chr12:104195000-104208600	Weak transcription	Left Ventricle	heart
29	chr12:104195000-104213800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:104195800-104208400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:104196000-104203600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:104196400-104200600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:104196400-104202200	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:104196400-104203400	Weak transcription	Fetal Stomach	stomach
35	chr12:104196400-104205000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:104196400-104213600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:104196400-104214800	Weak transcription	Brain Substantia Nigra	brain
38	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
39	chr12:104196600-104200800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr12:104196600-104200800	Weak transcription	Pancreas	Pancrea
41	chr12:104196600-104200800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:104196600-104202200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:104196600-104203600	Weak transcription	Brain Angular Gyrus	brain
44	chr12:104196600-104204200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:104196600-104206800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:104196600-104207800	Weak transcription	HSMMtube	muscle
47	chr12:104196600-104212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:104196600-104213000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:104196800-104200800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:104196800-104200800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links