Variant report

Variant	rs12199460
Chromosome Location	chr6:31094728-31094729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31081982..31084650-chr6:31092935..31096389,3	MCF-7	breast:
2	chr6:31090881..31093261-chr6:31094192..31096306,2	K562	blood:
3	chr6:31088197..31091806-chr6:31092941..31094886,3	K562	blood:
4	chr6:31093740..31096659-chr6:31097265..31098967,2	K562	blood:
5	chr6:31093836..31097468-chr6:31099358..31102420,4	K562	blood:
6	chr6:31075272..31076774-chr6:31094558..31097353,2	K562	blood:

Variant related genes	Relation type
ENSG00000204539	Chromatin interaction
ENSG00000204540	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12191286	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12195316	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12197796	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12201248	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12204500	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12214039	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13198298	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13201757	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13204986	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13212902	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17196961	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3734852	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3778639	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909111	0.82[ASN][1000 genomes]
rs6909321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6929464	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6931921	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6932086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756290	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	esv1797052	chr6:31083813-31095816	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	esv1820685	chr6:31083813-31097453	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	esv1799829	chr6:31087133-31097183	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12199460	XXbac-BPG248L24.12	cis	Artery Tibial	GTEx
rs12199460	XXbac-BPG248L24.12	cis	Thyroid	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31083200-31105400	Weak transcription	Spleen	Spleen
2	chr6:31088000-31094800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:31088000-31095000	Enhancers	HMEC	breast
4	chr6:31088200-31095000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:31089000-31096200	Enhancers	Lung	lung
6	chr6:31089600-31094800	Enhancers	NHEK	skin
7	chr6:31090000-31095800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:31091200-31096000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr6:31092200-31095200	Enhancers	Fetal Muscle Leg	muscle
10	chr6:31092400-31094800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:31092600-31096000	Enhancers	Stomach Mucosa	stomach
12	chr6:31092800-31095000	Enhancers	Left Ventricle	heart
13	chr6:31092800-31095200	Enhancers	Adipose Nuclei	Adipose
14	chr6:31092800-31095200	Enhancers	HSMM	muscle
15	chr6:31093000-31095000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:31093000-31096000	Enhancers	Gastric	stomach
17	chr6:31093000-31096000	Enhancers	Right Atrium	heart
18	chr6:31093000-31096000	Enhancers	Right Ventricle	heart
19	chr6:31093200-31094800	Enhancers	Esophagus	oesophagus
20	chr6:31093200-31094800	Enhancers	NHDF-Ad	bronchial
21	chr6:31093200-31096600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:31093400-31094800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:31093400-31095200	Enhancers	HSMMtube	muscle
24	chr6:31093400-31095800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:31093400-31105400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:31093400-31107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:31093600-31094800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:31093600-31094800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:31093600-31095000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:31093800-31095600	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:31093800-31097800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:31094000-31095400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:31094000-31095800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:31094000-31097000	Weak transcription	Pancreas	Pancrea
35	chr6:31094200-31094800	Enhancers	H1 Cell Line	embryonic stem cell
36	chr6:31094200-31095000	Enhancers	Fetal Intestine Small	intestine
37	chr6:31094200-31095000	Genic enhancers	Placenta Amnion	Placenta Amnion
38	chr6:31094200-31095200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr6:31094200-31096000	Enhancers	Duodenum Mucosa	Duodenum
40	chr6:31094400-31094800	Enhancers	Colonic Mucosa	Colon
41	chr6:31094400-31094800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr6:31094400-31095200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr6:31094400-31095200	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr6:31094400-31096000	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr6:31094600-31094800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:31094600-31095200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr6:31094600-31095200	Enhancers	K562	blood
48	chr6:31094600-31095800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:31094600-31099400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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