Variant report

Variant	rs3858254
Chromosome Location	chr10:6518505-6518506
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	chr10:6505761..6513673-chr10:6513705..6518581,11	K562	blood:
2	chr10:6515689..6518540-chr10:6536895..6539799,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1886050	0.81[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs1970926	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2026431	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2026432	0.80[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs2236379	0.81[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs3793729	0.81[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs587198	0.91[CHB][hapmap]
rs7089504	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs790815	0.87[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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6496600-6539200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr10:6498400-6537000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr10:6498600-6518800	Weak transcription	Fetal Stomach	stomach
4	chr10:6499000-6527800	Weak transcription	Pancreas	Pancrea
5	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
6	chr10:6501600-6527200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:6502200-6518800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:6503000-6533000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:6504600-6524200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:6506200-6520400	Weak transcription	Fetal Muscle Leg	muscle
12	chr10:6509200-6541200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:6509800-6533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:6514000-6540000	Weak transcription	Psoas Muscle	Psoas
16	chr10:6515000-6518800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr10:6515400-6520000	Enhancers	NHEK	skin
18	chr10:6516400-6518600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:6516400-6518600	Weak transcription	HMEC	breast
20	chr10:6516400-6518800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr10:6516400-6518800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:6516400-6535800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr10:6516600-6518800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr10:6516600-6523000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr10:6516800-6519000	Genic enhancers	Primary T cells from cord blood	blood
26	chr10:6517000-6518800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:6517000-6531800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr10:6517200-6518800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr10:6517200-6557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr10:6517400-6518600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:6517400-6520200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr10:6517400-6520600	Weak transcription	Brain Angular Gyrus	brain
33	chr10:6517400-6520800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr10:6517400-6523400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr10:6517400-6524200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr10:6517400-6524600	Strong transcription	Fetal Thymus	thymus
37	chr10:6517400-6525000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr10:6517400-6527000	Weak transcription	Brain Substantia Nigra	brain
39	chr10:6517400-6527800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr10:6517600-6519200	Genic enhancers	Dnd41	blood
41	chr10:6517600-6519600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:6517600-6539600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr10:6517600-6541800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr10:6517800-6519000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:6517800-6525000	Weak transcription	Brain Hippocampus Middle	brain
46	chr10:6518000-6518800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr10:6518000-6520000	Weak transcription	K562	blood
48	chr10:6518000-6524200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr10:6518200-6518600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:6518200-6519200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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