Variant report

Variant	rs2928401
Chromosome Location	chr10:50002557-50002558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49986976..49988548-chr10:50000055..50002559,2	MCF-7	breast:
2	chr10:49998728..50000919-chr10:50001573..50004326,2	K562	blood:
3	chr10:50000720..50003091-chr10:50019887..50021986,2	MCF-7	breast:
4	chr10:49998728..50000670-chr10:50000841..50003073,2	K562	blood:
5	chr10:50001590..50003527-chr10:50010221..50013133,2	MCF-7	breast:
6	chr10:50001268..50003610-chr10:50006671..50009349,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128815	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10776647	0.89[JPT][hapmap]
rs10776648	0.89[JPT][hapmap]
rs10857655	0.89[JPT][hapmap]
rs11101511	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11101529	0.89[JPT][hapmap]
rs11101530	0.89[JPT][hapmap]
rs11101531	0.88[JPT][hapmap]
rs1904596	0.89[JPT][hapmap]
rs2002588	0.89[JPT][hapmap]
rs2127590	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2170132	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2448539	0.88[JPT][hapmap]
rs2448540	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2448545	0.84[JPT][hapmap]
rs2457214	1.00[JPT][hapmap]
rs2620888	0.89[JPT][hapmap]
rs2620889	0.82[JPT][hapmap]
rs2620891	0.89[JPT][hapmap]
rs2620896	1.00[JPT][hapmap]
rs2620898	0.89[JPT][hapmap]
rs2620903	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2620904	0.89[JPT][hapmap]
rs2663031	1.00[YRI][hapmap]
rs2663035	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2663044	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2663053	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2928393	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2940704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940707	1.00[YRI][hapmap]
rs2943244	0.89[JPT][hapmap]
rs2947344	1.00[YRI][hapmap]
rs2947345	1.00[YRI][hapmap]
rs3747872	0.89[JPT][hapmap]
rs3747874	0.89[JPT][hapmap]
rs3747875	0.89[JPT][hapmap]
rs3860188	0.89[JPT][hapmap]
rs4838648	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537576	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7079766	0.89[JPT][hapmap]
rs726786	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7900138	0.89[JPT][hapmap]
rs7913005	0.89[JPT][hapmap]
rs877819	0.89[JPT][hapmap]

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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831865	chr10:49994254-50164239	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3387538	chr10:50002236-50002677	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49967800-50006800	Strong transcription	Primary B cells from peripheral blood	blood
2	chr10:49981400-50007200	Strong transcription	Primary B cells from cord blood	blood
3	chr10:49982600-50006800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr10:49992800-50005200	Strong transcription	Primary hematopoietic stem cells	blood
5	chr10:49993800-50005600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:49996600-50005400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:49999200-50005600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr10:49999200-50006200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr10:49999400-50003400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:49999600-50003000	Enhancers	Left Ventricle	heart
11	chr10:49999800-50003000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr10:49999800-50003200	Enhancers	HMEC	breast
13	chr10:50000000-50003000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:50000000-50003200	Enhancers	NHEK	skin
15	chr10:50000000-50008400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr10:50000400-50008400	Weak transcription	Colonic Mucosa	Colon
17	chr10:50001000-50003800	Weak transcription	Lung	lung
18	chr10:50001000-50008200	Weak transcription	Fetal Thymus	thymus
19	chr10:50001000-50012800	Weak transcription	Right Ventricle	heart
20	chr10:50001200-50005600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:50001200-50009400	Weak transcription	Fetal Muscle Leg	muscle
22	chr10:50001400-50007600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:50001600-50008200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr10:50002200-50003000	Genic enhancers	Spleen	Spleen
25	chr10:50002200-50003800	Weak transcription	GM12878-XiMat	blood

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