Variant report

Variant	rs12409493
Chromosome Location	chr1:151773167-151773168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151771040..151773951-chr1:151782694..151784484,3	K562	blood:
2	chr1:151770881..151774367-chr1:151786518..151790478,5	MCF-7	breast:
3	chr1:151773064..151773919-chr1:151809447..151809983,2	MCF-7	breast:
4	chr1:151770963..151775334-chr1:151775936..151780512,5	MCF-7	breast:
5	chr1:151728568..151732479-chr1:151772767..151776235,3	K562	blood:
6	chr1:151771155..151774343-chr1:151777363..151779853,3	MCF-7	breast:
7	chr1:151763150..151767122-chr1:151771180..151776437,5	K562	blood:
8	chr1:151771964..151773618-chr1:151776379..151779150,2	K562	blood:
9	chr1:151772358..151773986-chr1:151801710..151803954,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000182134	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000236940	Chromatin interaction
ENSG00000213171	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10888435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204885	0.81[JPT][hapmap]
rs11204887	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204888	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12066445	0.93[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]
rs12073999	0.89[EUR][1000 genomes]
rs12567867	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781419	0.88[CEU][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs2293088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33911740	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748612	0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs3923394	0.84[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs4845572	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6667279	0.91[EUR][1000 genomes]
rs6679233	0.88[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap]
rs7534811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868868	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9017	0.96[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs9826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12409493	S100A13	cis	cerebellum	SCAN
rs12409493	TDRKH	Cis_1M	lymphoblastoid	RTeQTL
rs12409493	LINGO4	cis	cerebellum	SCAN
rs12409493	TDRKH	cis	cerebellum	SCAN
rs12409493	SNX27	cis	Esophagus Mucosa	GTEx
rs12409493	BCL9	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151764200-151778800	Weak transcription	Pancreas	Pancrea
2	chr1:151764200-151779600	Weak transcription	Gastric	stomach
3	chr1:151764200-151787000	Weak transcription	Right Ventricle	heart
4	chr1:151764200-151792800	Weak transcription	Lung	lung
5	chr1:151764400-151779200	Weak transcription	Liver	Liver
6	chr1:151764400-151779800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:151764600-151779400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:151764600-151779400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:151764600-151782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:151764600-151787600	Weak transcription	Primary T cells from cord blood	blood
11	chr1:151765000-151779400	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:151765400-151784200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:151766000-151780200	Weak transcription	Dnd41	blood
14	chr1:151770400-151776200	Weak transcription	Spleen	Spleen
15	chr1:151770800-151787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:151771400-151773400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:151771400-151773600	Enhancers	Fetal Thymus	thymus
18	chr1:151771400-151778200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:151771600-151773200	Enhancers	Placenta	Placenta
20	chr1:151772000-151774200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:151772200-151773600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr1:151772200-151777600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:151772400-151773400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:151772600-151773400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:151772800-151773200	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:151772800-151773200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:151772800-151773400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr1:151772800-151773400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:151772800-151773400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:151772800-151773400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:151772800-151773400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:151772800-151773600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:151773000-151773600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:151773000-151773600	Enhancers	Thymus	Thymus
35	chr1:151773000-151778600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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