Variant report

Variant	rs2274385
Chromosome Location	chr13:39585178-39585179
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	chr13:39584395..39587085-chr13:39611673..39614003,2	MCF-7	breast:
2	chr13:39583306..39585732-chr13:39594165..39596602,2	K562	blood:

Variant related genes	Relation type
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11147745	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429338	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12430450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12431316	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1326405	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.96[ASN][1000 genomes]
rs17058947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17059014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2094252	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2094253	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2094254	0.99[ASN][1000 genomes]
rs2104518	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2274384	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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34316151	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34327528	0.99[ASN][1000 genomes]
rs35804724	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs35864330	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751377	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751378	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4142398	0.86[ASN][1000 genomes]
rs55809136	0.96[ASN][1000 genomes]
rs66496062	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66908302	0.98[ASN][1000 genomes]
rs67296293	0.98[ASN][1000 genomes]
rs73169457	0.99[ASN][1000 genomes]
rs7317852	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7318688	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7327748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs747752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7987207	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.98[ASN][1000 genomes]
rs7994530	0.88[ASN][1000 genomes]
rs7997052	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.97[ASN][1000 genomes]
rs7998475	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8000929	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9566385	0.87[ASN][1000 genomes]
rs9566389	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566391	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9566393	0.86[ASN][1000 genomes]
rs9566396	0.86[ASN][1000 genomes]
rs9576669	0.92[ASW][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs9576670	0.98[ASN][1000 genomes]
rs9576673	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9576674	0.98[ASN][1000 genomes]
rs9576676	0.98[ASN][1000 genomes]
rs9576677	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9576678	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9576679	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs9576681	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9576683	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9576684	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9576685	0.99[ASN][1000 genomes]
rs9576686	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576688	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576690	0.98[ASN][1000 genomes]
rs9576691	0.82[ASN][1000 genomes]
rs9576692	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576693	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576695	0.99[ASN][1000 genomes]
rs9576696	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9576697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576700	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576701	0.96[ASN][1000 genomes]
rs9576703	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9576705	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9576707	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9576710	0.92[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs9576711	0.92[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs9576717	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv977227	chr13:39584329-39585449	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2274385	LHFP	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39580800-39586200	Weak transcription	Colonic Mucosa	Colon
2	chr13:39581400-39585400	Weak transcription	Fetal Intestine Small	intestine
3	chr13:39581600-39590800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:39581600-39592000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr13:39581600-39592400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:39581800-39585400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:39581800-39589400	Strong transcription	Brain Germinal Matrix	brain
8	chr13:39581800-39592200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:39581800-39593200	Strong transcription	HSMM	muscle
10	chr13:39581800-39597000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr13:39582000-39588000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr13:39582000-39596600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr13:39582000-39608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:39582200-39590800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:39582200-39592600	Strong transcription	Fetal Thymus	thymus
16	chr13:39582200-39593400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr13:39582200-39596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr13:39582200-39596800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr13:39582200-39597400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:39582400-39590400	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:39582400-39590400	Strong transcription	GM12878-XiMat	blood
22	chr13:39582400-39605400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr13:39582600-39586000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:39582600-39589600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr13:39582600-39592000	Strong transcription	Placenta	Placenta
26	chr13:39582600-39592400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr13:39582600-39592400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr13:39582800-39593600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr13:39583000-39585400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr13:39583000-39585400	Weak transcription	Right Ventricle	heart
31	chr13:39583000-39592400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:39583200-39592400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:39583200-39592400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr13:39583200-39592400	Strong transcription	Adipose Nuclei	Adipose
35	chr13:39583200-39593200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr13:39583200-39606600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr13:39583400-39585600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr13:39583400-39586800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr13:39583400-39587000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr13:39583400-39587600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr13:39583400-39592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr13:39583400-39592600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:39583400-39593200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr13:39583600-39585200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr13:39583600-39586800	Weak transcription	Small Intestine	intestine
46	chr13:39583600-39587400	Weak transcription	Psoas Muscle	Psoas
47	chr13:39583600-39597200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr13:39583800-39585400	Strong transcription	Liver	Liver
49	chr13:39583800-39592400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:39583800-39592600	Strong transcription	Primary T cells fromperipheralblood	blood

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