Variant report

Variant	rs11111793
Chromosome Location	chr12:104198118-104198119
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr12:104197998-104198298	K562	blood:	n/a	chr12:104198001-104198010

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104197681..104199804-chr12:104233310..104235105,2	K562	blood:
2	chr12:104192525..104200371-chr12:104233987..104238967,10	MCF-7	breast:
3	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:
4	chr12:104194168..104195687-chr12:104197418..104199673,2	K562	blood:
5	chr12:104197525..104199804-chr12:104233310..104236273,2	K562	blood:
6	chr12:104196315..104200600-chr12:104233023..104235965,5	MCF-7	breast:
7	chr12:104163207..104165311-chr12:104196733..104198239,2	K562	blood:
8	chr12:104190724..104195360-chr12:104196501..104199658,6	MCF-7	breast:

No data

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

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10861104	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861105	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10861109	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111765	0.80[ASN][1000 genomes]
rs11111771	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11111778	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11111786	0.87[EUR][1000 genomes]
rs11111788	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11111789	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11111791	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111792	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111795	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111796	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11111799	0.87[ASN][1000 genomes]
rs11610714	0.87[ASN][1000 genomes]
rs12228207	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12229276	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12830701	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1866292	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1866295	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2033774	0.86[AFR][1000 genomes]
rs34307072	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35371470	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35746861	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35945096	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36034617	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3751204	0.80[ASN][1000 genomes]
rs3812803	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3935416	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964289	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964623	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964780	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964794	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4964805	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4964806	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4964812	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4964823	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4964827	0.81[ASN][1000 genomes]
rs67825151	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134701	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs869993	0.81[ASN][1000 genomes]
rs954920	0.80[ASN][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
rs11111793	RP11-341G23.4	cis	Thyroid	GTEx
rs11111793	RP11-341G23.4	cis	Artery Tibial	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	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:104185800-104198800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:104187400-104206800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:104187800-104198200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
10	chr12:104190800-104198800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:104190800-104201800	Weak transcription	Gastric	stomach
12	chr12:104190800-104204400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:104192000-104200400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:104192600-104206600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:104192800-104199600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:104193600-104204000	Weak transcription	Primary T cells from cord blood	blood
20	chr12:104193800-104198200	Genic enhancers	K562	blood
21	chr12:104194000-104206800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:104194400-104207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:104194600-104198800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:104194600-104199400	Weak transcription	Esophagus	oesophagus
25	chr12:104194600-104199600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:104194600-104199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:104194600-104203800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:104194600-104207000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:104194600-104214600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:104194600-104214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:104194800-104207200	Weak transcription	Adipose Nuclei	Adipose
32	chr12:104194800-104215200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:104195000-104198400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:104195000-104198600	Weak transcription	Placenta	Placenta
35	chr12:104195000-104199000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:104195000-104200800	Weak transcription	Spleen	Spleen
37	chr12:104195000-104201800	Weak transcription	Stomach Mucosa	stomach
38	chr12:104195000-104203600	Weak transcription	Fetal Intestine Large	intestine
39	chr12:104195000-104204400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:104195000-104205200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:104195000-104207800	Weak transcription	Fetal Lung	lung
42	chr12:104195000-104208600	Weak transcription	Left Ventricle	heart
43	chr12:104195000-104213800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:104195200-104199600	Weak transcription	Liver	Liver
45	chr12:104195400-104198200	Genic enhancers	Colon Smooth Muscle	Colon
46	chr12:104195600-104199000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:104195600-104199600	Weak transcription	Primary B cells from cord blood	blood
48	chr12:104195800-104198800	Weak transcription	Ovary	ovary
49	chr12:104195800-104208400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:104196000-104199600	Weak transcription	Fetal Intestine Small	intestine

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