Variant report

Variant	rs12208229
Chromosome Location	chr6:36350424-36350425
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:36349379-36350571	GM12878	blood:	n/a	n/a
2	WRNIP1	chr6:36350394-36350505	GM12878	blood:	n/a	n/a
3	MTA3	chr6:36349272-36350658	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36269156..36270741-chr6:36349909..36351780,2	MCF-7	breast:
2	chr6:36323097..36324990-chr6:36349232..36352025,2	MCF-7	breast:
3	chr6:36350329..36353263-chr6:36561816..36565037,3	MCF-7	breast:
4	chr6:36350010..36352729-chr6:36563870..36566788,2	MCF-7	breast:
5	chr6:36350275..36352895-chr6:36574833..36577389,2	MCF-7	breast:
6	chr6:36344497..36346225-chr6:36349695..36351527,2	K562	blood:
7	chr6:36350050..36352863-chr6:36645939..36648459,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224666	TF binding region
ENSG00000124762	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12203115	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12525283	1.00[JPT][hapmap]
rs17356524	1.00[CHB][hapmap]
rs17715809	1.00[JPT][hapmap]
rs7754042	1.00[CHB][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	nsv428481	chr6:36219000-36365746	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12208229	LEMD2	cis	cerebellum	SCAN
rs12208229	FANCD2	trans	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36326800-36354000	Weak transcription	Small Intestine	intestine
2	chr6:36327000-36354000	Weak transcription	Right Atrium	heart
3	chr6:36328400-36351200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:36328400-36353400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:36328800-36353600	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:36333200-36353800	Weak transcription	Pancreas	Pancrea
7	chr6:36333800-36353600	Weak transcription	Stomach Mucosa	stomach
8	chr6:36334600-36351000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:36339200-36354200	Weak transcription	Esophagus	oesophagus
10	chr6:36339800-36353600	Weak transcription	Lung	lung
11	chr6:36341600-36350800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:36341800-36350800	Weak transcription	Spleen	Spleen
13	chr6:36344200-36354000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:36345000-36351000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:36345400-36351800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:36346800-36351000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:36347200-36351000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:36349000-36350600	Weak transcription	Fetal Intestine Small	intestine
19	chr6:36349000-36350600	Flanking Active TSS	GM12878-XiMat	blood
20	chr6:36349000-36351600	Weak transcription	NHEK	skin
21	chr6:36349400-36350800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:36349400-36350800	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:36349800-36352000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:36350200-36350800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:36350200-36351200	Enhancers	Aorta	Aorta
26	chr6:36350400-36350600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:36350400-36350600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:36350400-36350800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr6:36350400-36350800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:36350400-36352000	Enhancers	Primary T helper cells PMA-I stimulated	--

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