Variant report

Variant	rs12207548
Chromosome Location	chr6:36656256-36656257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
2	chr6:36650647..36652675-chr6:36655883..36658117,2	MCF-7	breast:
3	chr6:36656125..36657871-chr6:36725735..36728109,2	MCF-7	breast:
4	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
5	chr6:36645354..36650870-chr6:36653418..36656910,6	K562	blood:
6	chr6:36655048..36657495-chr6:36690151..36694122,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263894	Chromatin interaction
ENSG00000124762	Chromatin interaction
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12191972	0.90[CEU][hapmap]
rs3176352	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457931	0.82[CHB][hapmap]
rs7767246	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12207548	C6orf106	cis	parietal	SCAN
rs12207548	GLP1R	cis	cerebellum	SCAN
rs12207548	STK38	cis	parietal	SCAN
rs12207548	C6orf81	cis	parietal	SCAN
rs12207548	SNRPC	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36650400-36656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36650800-36659600	Weak transcription	Right Atrium	heart
3	chr6:36651200-36660000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:36651600-36657000	Enhancers	Primary B cells from cord blood	blood
5	chr6:36651600-36659200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:36651800-36656800	Strong transcription	Fetal Intestine Small	intestine
7	chr6:36651800-36658800	Weak transcription	Fetal Heart	heart
8	chr6:36653400-36656800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:36653800-36657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:36654000-36656400	Weak transcription	Psoas Muscle	Psoas
11	chr6:36654200-36659400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:36654600-36656400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:36654600-36659400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:36654600-36659600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:36654600-36659600	Weak transcription	Fetal Thymus	thymus
16	chr6:36654800-36656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:36654800-36656400	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:36654800-36659600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:36654800-36660200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:36655000-36656600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:36655000-36656600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:36655000-36656600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:36655000-36656600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:36655000-36656600	Weak transcription	Brain Anterior Caudate	brain
25	chr6:36655000-36656800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:36655000-36656800	Weak transcription	Brain Angular Gyrus	brain
27	chr6:36655000-36656800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:36655000-36657000	Weak transcription	Small Intestine	intestine
29	chr6:36655000-36657600	Weak transcription	HepG2	liver
30	chr6:36655000-36657800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr6:36655000-36658400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:36655000-36658800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:36655000-36658800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:36655000-36659200	Weak transcription	Spleen	Spleen
35	chr6:36655000-36659400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:36655000-36659400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:36655000-36659600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:36655000-36659600	Weak transcription	Right Ventricle	heart
39	chr6:36655000-36660000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:36655000-36660000	Weak transcription	Pancreas	Pancrea
41	chr6:36655000-36660200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr6:36655000-36660200	Weak transcription	Thymus	Thymus
43	chr6:36655000-36660400	Weak transcription	Stomach Mucosa	stomach
44	chr6:36655000-36672000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:36655200-36656800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:36655200-36656800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:36655200-36656800	Weak transcription	Brain Substantia Nigra	brain
48	chr6:36655200-36656800	Weak transcription	A549	lung
49	chr6:36655200-36657000	Weak transcription	NHLF	lung
50	chr6:36655200-36657200	Weak transcription	Liver	Liver

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