Variant report

Variant	rs11900317
Chromosome Location	chr2:47484138-47484139
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47478646..47481044-chr2:47483765..47486319,2	MCF-7	breast:
2	chr2:47399035..47407354-chr2:47479551..47494841,29	MCF-7	breast:
3	chr2:47400516..47406880-chr2:47471949..47486822,24	K562	blood:
4	chr2:47401545..47404971-chr2:47483615..47487701,5	MCF-7	breast:
5	chr2:47399224..47401292-chr2:47482890..47486794,3	MCF-7	breast:
6	chr2:47473511..47478428-chr2:47483950..47488018,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10172988	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[ASN][1000 genomes]
rs10185578	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs10186190	0.94[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10190105	0.84[ASN][1000 genomes]
rs10190217	0.95[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10209637	0.83[CHB][hapmap];0.93[CHD][hapmap]
rs10209762	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10210258	0.83[EUR][1000 genomes]
rs11125127	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11894768	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896275	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12612772	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12618281	0.91[ASN][1000 genomes]
rs1553061	0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.84[ASN][1000 genomes]
rs17036412	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2036164	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2055225	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap]
rs4953481	0.83[CHB][hapmap]
rs6727256	0.86[ASN][1000 genomes]
rs6738753	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6751203	0.95[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6755555	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72806423	0.80[ASN][1000 genomes]
rs7595256	0.85[ASN][1000 genomes]
rs931639	0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.84[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3393036	chr2:47482098-47484471	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11900317	STON1-GTF2A1L	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47477000-47491400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:47477200-47491200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:47478800-47487400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:47478800-47496400	Weak transcription	Hela-S3	cervix
5	chr2:47480000-47486600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:47482200-47485000	Weak transcription	GM12878-XiMat	blood
7	chr2:47482400-47489400	Weak transcription	Fetal Intestine Small	intestine
8	chr2:47482400-47491400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:47483400-47484200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:47483400-47484200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:47483400-47484200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:47483400-47484400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:47483400-47484600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr2:47483400-47484600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:47483400-47484600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:47483400-47485200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:47483400-47485600	Enhancers	HSMM	muscle
18	chr2:47483400-47485800	Enhancers	HSMMtube	muscle
19	chr2:47483600-47484200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr2:47483600-47484200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:47483600-47484200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:47483600-47484200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:47483600-47484200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:47483600-47484200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:47483600-47484200	Enhancers	Brain Angular Gyrus	brain
26	chr2:47483600-47484200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr2:47483600-47484200	Enhancers	NH-A	brain
28	chr2:47483600-47484400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr2:47483600-47484400	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:47483600-47484400	Enhancers	A549	lung
31	chr2:47483600-47484400	Bivalent Enhancer	HepG2	liver
32	chr2:47483800-47484200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr2:47483800-47484200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr2:47483800-47484200	Enhancers	Fetal Muscle Trunk	muscle
35	chr2:47483800-47484400	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr2:47483800-47484400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:47483800-47484400	Enhancers	Fetal Kidney	kidney
38	chr2:47483800-47485200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:47483800-47492000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:47484000-47484200	Enhancers	Fetal Intestine Large	intestine
41	chr2:47484000-47484400	Enhancers	Brain Hippocampus Middle	brain
42	chr2:47484000-47487200	Weak transcription	Spleen	Spleen
43	chr2:47484000-47487800	Weak transcription	Placenta	Placenta

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