Variant report

Variant	rs9576693
Chromosome Location	chr13:39582048-39582049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39581808..39584670-chr13:39588176..39590668,3	K562	blood:
2	chr13:39581567..39584670-chr13:39588176..39591409,3	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11147745	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12428445	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12429324	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12429338	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12430450	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12431316	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1326405	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17058947	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17058990	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17059014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2094252	0.98[ASN][1000 genomes]
rs2094253	0.98[ASN][1000 genomes]
rs2094254	0.98[ASN][1000 genomes]
rs2104518	0.98[ASN][1000 genomes]
rs2274384	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2274385	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296648	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34316151	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34327528	0.98[ASN][1000 genomes]
rs35804724	0.93[ASN][1000 genomes]
rs35864330	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751377	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751378	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751379	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4142398	0.83[ASN][1000 genomes]
rs55809136	0.93[ASN][1000 genomes]
rs66496062	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66908302	0.97[ASN][1000 genomes]
rs67296293	0.97[ASN][1000 genomes]
rs73169457	0.98[ASN][1000 genomes]
rs7317852	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7318688	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7327748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs747752	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7987207	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7994530	0.85[ASN][1000 genomes]
rs7997052	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs7998475	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8000929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9566385	0.86[ASN][1000 genomes]
rs9566389	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9566391	0.93[ASN][1000 genomes]
rs9566393	0.83[ASN][1000 genomes]
rs9566396	0.83[ASN][1000 genomes]
rs9576669	0.87[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs9576670	0.97[ASN][1000 genomes]
rs9576673	0.95[ASN][1000 genomes]
rs9576674	0.97[ASN][1000 genomes]
rs9576676	0.97[ASN][1000 genomes]
rs9576677	0.97[ASN][1000 genomes]
rs9576678	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs9576679	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9576681	0.98[ASN][1000 genomes]
rs9576683	0.98[ASN][1000 genomes]
rs9576684	0.98[ASN][1000 genomes]
rs9576685	0.98[ASN][1000 genomes]
rs9576686	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576688	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576690	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9576691	0.81[ASN][1000 genomes]
rs9576692	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576695	0.98[ASN][1000 genomes]
rs9576696	0.97[ASN][1000 genomes]
rs9576697	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576698	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576699	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576700	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576701	0.93[ASN][1000 genomes]
rs9576703	0.91[ASN][1000 genomes]
rs9576705	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9576707	0.93[ASN][1000 genomes]
rs9576710	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9576711	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9576717	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9576693	LHFP	cis	cerebellum	SCAN
rs9576693	C13orf23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39571600-39583800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:39572200-39584600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr13:39573400-39584800	Weak transcription	K562	blood
4	chr13:39574600-39585000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:39577000-39584600	Weak transcription	Left Ventricle	heart
6	chr13:39579000-39585000	Weak transcription	Gastric	stomach
7	chr13:39579600-39582400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr13:39580000-39582400	Weak transcription	Primary T cells from cord blood	blood
9	chr13:39580000-39584400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr13:39580000-39584400	Weak transcription	Dnd41	blood
11	chr13:39580200-39582200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr13:39580200-39584400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:39580200-39584400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:39580200-39584600	Weak transcription	Fetal Muscle Leg	muscle
15	chr13:39580200-39584800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:39580200-39585000	Weak transcription	Fetal Stomach	stomach
17	chr13:39580200-39585000	Weak transcription	NH-A	brain
18	chr13:39580400-39582600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr13:39580400-39584600	Weak transcription	Fetal Brain Female	brain
20	chr13:39580400-39585000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:39580400-39585000	Weak transcription	Lung	lung
22	chr13:39580600-39582200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:39580600-39582200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr13:39580600-39582200	Weak transcription	Fetal Thymus	thymus
25	chr13:39580600-39583200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr13:39580600-39584400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr13:39580800-39582400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr13:39580800-39582400	Weak transcription	GM12878-XiMat	blood
29	chr13:39580800-39582400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr13:39580800-39582600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr13:39580800-39583000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:39580800-39583200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:39580800-39584400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr13:39580800-39584400	Weak transcription	Fetal Lung	lung
35	chr13:39580800-39584800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:39580800-39584800	Weak transcription	Colon Smooth Muscle	Colon
37	chr13:39580800-39586200	Weak transcription	Colonic Mucosa	Colon
38	chr13:39581000-39582600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr13:39581000-39582600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:39581000-39582600	Weak transcription	Placenta	Placenta
41	chr13:39581000-39582800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:39581000-39583200	Weak transcription	Adipose Nuclei	Adipose
43	chr13:39581000-39584200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr13:39581000-39584400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr13:39581000-39584600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr13:39581000-39584600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:39581200-39582800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr13:39581200-39583400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr13:39581200-39583800	Weak transcription	Liver	Liver
50	chr13:39581200-39584400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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