Variant report

Variant	rs2274384
Chromosome Location	chr13:39618174-39618175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:39613981..39615721-chr13:39616266..39619122,2	K562	blood:
2	chr13:39610419..39613692-chr13:39616080..39618520,4	K562	blood:
3	chr13:39604794..39607526-chr13:39617975..39619504,2	K562	blood:

Variant related genes	Relation type
ENSG00000188811	Chromatin interaction
ENSG00000120685	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1109625	1.00[CEU][hapmap]
rs11147745	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12428445	0.92[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12429324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12429338	0.92[ASN][1000 genomes]
rs12430450	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12431316	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1326405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17058947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17058990	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17059014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2094252	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2094253	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2094254	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2104518	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2274385	0.92[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs2296648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs34316151	0.91[ASN][1000 genomes]
rs34327528	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35804724	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35864330	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3751377	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3751378	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3751379	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3812879	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4142398	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55809136	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66496062	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs66908302	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67296293	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73169457	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7317852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7318688	0.96[ASN][1000 genomes]
rs7327748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs747752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7987207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7994530	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7998475	0.91[ASN][1000 genomes]
rs8000929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9566385	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9566389	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9566391	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9566393	0.94[ASN][1000 genomes]
rs9566396	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566397	0.86[ASN][1000 genomes]
rs9576666	1.00[CEU][hapmap]
rs9576669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs9576670	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9576673	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9576674	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9576676	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9576677	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9576678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9576679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9576681	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576683	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576684	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576685	0.91[ASN][1000 genomes]
rs9576686	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9576688	0.91[ASN][1000 genomes]
rs9576690	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9576691	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9576692	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9576693	0.89[ASN][1000 genomes]
rs9576695	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576696	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576697	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9576698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9576699	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9576700	0.92[ASN][1000 genomes]
rs9576701	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576703	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576707	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576710	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576717	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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
rs2274384	LHFP	cis	cerebellum	SCAN
rs2274384	C13orf23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39613000-39629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:39613000-39636200	Weak transcription	Spleen	Spleen
3	chr13:39613200-39622200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:39613200-39626600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:39613200-39636400	Weak transcription	Gastric	stomach
6	chr13:39613200-39637200	Weak transcription	Pancreas	Pancrea
7	chr13:39613200-39647000	Weak transcription	Left Ventricle	heart
8	chr13:39613200-39647200	Weak transcription	Lung	lung
9	chr13:39613400-39620600	Weak transcription	Psoas Muscle	Psoas
10	chr13:39613400-39622400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr13:39613400-39625000	Weak transcription	HSMMtube	muscle
12	chr13:39613400-39646600	Weak transcription	Aorta	Aorta
13	chr13:39613600-39618200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:39613600-39623400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr13:39613600-39625200	Weak transcription	NHLF	lung
16	chr13:39613600-39626600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr13:39613600-39626600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr13:39613600-39629000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr13:39613600-39629200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr13:39613600-39629800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr13:39613800-39618200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr13:39613800-39618200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:39613800-39618200	Weak transcription	Brain Anterior Caudate	brain
24	chr13:39613800-39619200	Weak transcription	NH-A	brain
25	chr13:39613800-39620400	Weak transcription	Stomach Mucosa	stomach
26	chr13:39613800-39621000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:39613800-39621400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr13:39613800-39622400	Weak transcription	HSMM	muscle
29	chr13:39613800-39623200	Weak transcription	HMEC	breast
30	chr13:39613800-39627000	Weak transcription	Brain Substantia Nigra	brain
31	chr13:39613800-39639200	Weak transcription	Fetal Stomach	stomach
32	chr13:39614000-39625400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr13:39614000-39627000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr13:39614000-39627000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:39614000-39628400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:39614000-39634400	Weak transcription	Fetal Kidney	kidney
37	chr13:39614200-39618200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr13:39614400-39620200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr13:39614400-39644000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:39614600-39619800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr13:39614600-39623800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr13:39615000-39618200	Weak transcription	Brain Hippocampus Middle	brain
43	chr13:39615000-39618200	Weak transcription	Fetal Brain Female	brain
44	chr13:39615000-39618200	Weak transcription	Fetal Intestine Large	intestine
45	chr13:39615000-39618200	Weak transcription	Placenta	Placenta
46	chr13:39615000-39618800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr13:39615000-39620000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:39615000-39621200	Weak transcription	Fetal Heart	heart
49	chr13:39615000-39621600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr13:39615000-39621800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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