Variant report

Variant	rs2545841
Chromosome Location	chr5:94905378-94905379
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	chr5:94889255..94892254-chr5:94902983..94905843,2	K562	blood:

Variant related genes	Relation type
ENSG00000164291	Chromatin interaction
ENSG00000198677	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10053324	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10076499	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1183640	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1541798	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1981952	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245588	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255165	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548652	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2560257	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560258	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560260	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2560261	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2560274	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731825	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2731826	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2731833	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2881976	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6556870	0.87[ASN][1000 genomes]
rs73777211	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9314148	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830408	chr5:94894032-94915995	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv598955	chr5:94903453-95136019	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94892000-94906200	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:94892200-94906000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:94892200-94906800	Weak transcription	Fetal Kidney	kidney
4	chr5:94892200-94907200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:94892200-94907400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:94892200-94934400	Weak transcription	Fetal Stomach	stomach
7	chr5:94892200-94936600	Weak transcription	Fetal Lung	lung
8	chr5:94892400-94905600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:94892400-94905800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:94892400-94906000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:94892400-94906600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:94892400-94907600	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:94892400-94908800	Weak transcription	HepG2	liver
14	chr5:94892400-94910200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:94892400-94911200	Weak transcription	HMEC	breast
16	chr5:94892400-94921000	Weak transcription	Psoas Muscle	Psoas
17	chr5:94892400-94922400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr5:94892400-94926000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:94892400-94926200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:94892400-94926200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:94892400-94926200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:94892400-94926600	Weak transcription	NH-A	brain
23	chr5:94892400-94937200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:94892600-94907800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:94894000-94908400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:94894000-94919000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:94898200-94926000	Weak transcription	Thymus	Thymus
28	chr5:94898400-94906600	Weak transcription	Brain Angular Gyrus	brain
29	chr5:94900200-94908000	Weak transcription	Placenta	Placenta
30	chr5:94900400-94910200	Weak transcription	Spleen	Spleen
31	chr5:94900400-94942400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:94900600-94906400	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:94900600-94913200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:94900600-94919600	Weak transcription	K562	blood
35	chr5:94900600-94921200	Weak transcription	Pancreas	Pancrea
36	chr5:94901000-94916400	Weak transcription	Fetal Brain Male	brain
37	chr5:94901400-94906200	Strong transcription	Primary T cells from cord blood	blood
38	chr5:94901400-94910200	Weak transcription	HSMM	muscle
39	chr5:94901600-94926400	Weak transcription	HUVEC	blood vessel
40	chr5:94901800-94909600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:94902000-94925800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:94902000-94936600	Weak transcription	HSMMtube	muscle
43	chr5:94902200-94906400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr5:94902400-94905600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr5:94902400-94906200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:94902600-94906400	Strong transcription	Primary B cells from cord blood	blood
47	chr5:94902800-94905400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:94902800-94906200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr5:94903000-94906200	Strong transcription	Fetal Thymus	thymus
50	chr5:94903200-94911800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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