Variant report

Variant	rs9826
Chromosome Location	chr1:151778899-151778900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151752426..151754254-chr1:151778758..151780979,2	K562	blood:

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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204885	0.81[JPT][hapmap]
rs11204887	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204888	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12066445	0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs12073999	0.89[EUR][1000 genomes]
rs12409493	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]
rs12567867	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781419	0.87[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs2293088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33911740	0.96[AMR][1000 genomes];0.98[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	0.94[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];0.93[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];0.99[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];0.90[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9017	0.96[CEU][hapmap];0.98[TSI][hapmap];0.99[EUR][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
rs9826	BCL9	cis	cerebellum	SCAN
rs9826	TDRKH	cis	cerebellum	SCAN
rs9826	TDRKH	Cis_1M	lymphoblastoid	RTeQTL
rs9826	S100A13	cis	cerebellum	SCAN
rs9826	LINGO4	cis	cerebellum	SCAN
rs9826	SNX27	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151764200-151779600	Weak transcription	Gastric	stomach
2	chr1:151764200-151787000	Weak transcription	Right Ventricle	heart
3	chr1:151764200-151792800	Weak transcription	Lung	lung
4	chr1:151764400-151779200	Weak transcription	Liver	Liver
5	chr1:151764400-151779800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:151764600-151779400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:151764600-151779400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:151764600-151782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:151764600-151787600	Weak transcription	Primary T cells from cord blood	blood
10	chr1:151765000-151779400	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:151765400-151784200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:151766000-151780200	Weak transcription	Dnd41	blood
13	chr1:151770800-151787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:151773200-151784800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:151773400-151784800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:151773400-151785000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:151774600-151787000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:151775800-151783600	Weak transcription	Psoas Muscle	Psoas
19	chr1:151776200-151779800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:151776600-151787200	Weak transcription	Spleen	Spleen
21	chr1:151777800-151780200	Weak transcription	Brain Anterior Caudate	brain
22	chr1:151778000-151779600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:151778000-151781800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:151778400-151786000	Strong transcription	Thymus	Thymus
25	chr1:151778400-151792800	Weak transcription	Left Ventricle	heart
26	chr1:151778600-151779000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:151778600-151779000	Genic enhancers	Fetal Thymus	thymus
28	chr1:151778600-151792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:151778600-151802400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:151778800-151779000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:151778800-151779000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:151778800-151779000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:151778800-151779000	Genic enhancers	Pancreas	Pancrea
34	chr1:151778800-151782600	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:151778800-151789200	Weak transcription	Fetal Intestine Small	intestine

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