Variant report

Variant	rs2293088
Chromosome Location	chr1:151777651-151777652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151774351..151777755-chr1:151779800..151782368,3	K562	blood:
2	chr1:151762360..151764432-chr1:151777142..151778868,2	MCF-7	breast:
3	chr1:151774281..151778666-chr1:151812036..151815315,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201134	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000234614	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10888435	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204885	0.81[JPT][hapmap]
rs11204887	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204888	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12066445	0.88[CEU][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs12073999	0.89[EUR][1000 genomes]
rs12409493	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]
rs12567867	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781419	0.84[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs33911740	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748612	0.88[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs3923394	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs4845572	0.90[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];0.81[JPT][hapmap]
rs7534811	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]
rs868868	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9017	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs9826	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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2293088	TDRKH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 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	chr1:151770800-151787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:151771400-151778200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:151773000-151778600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:151773200-151784800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:151773400-151784800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:151773400-151785000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:151774600-151787000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:151775800-151783600	Weak transcription	Psoas Muscle	Psoas
22	chr1:151776200-151779800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:151776600-151778400	Weak transcription	Thymus	Thymus
24	chr1:151776600-151778800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:151776600-151787200	Weak transcription	Spleen	Spleen
26	chr1:151777400-151778600	Enhancers	Fetal Thymus	thymus
27	chr1:151777600-151777800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:151777600-151777800	Enhancers	Brain Anterior Caudate	brain
29	chr1:151777600-151777800	Bivalent Enhancer	Fetal Intestine Small	intestine
30	chr1:151777600-151778000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr1:151777600-151778000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
32	chr1:151777600-151778200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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