Variant report

Variant	rs667254
Chromosome Location	chr10:6564775-6564776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2387407	0.82[JPT][hapmap]
rs500766	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519349	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs521153	1.00[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs563798	0.85[JPT][hapmap]
rs586355	0.85[JPT][hapmap]
rs591397	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs627715	0.85[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs667254	AKR1CL1	cis	parietal	SCAN
rs667254	GATA3	cis	parietal	SCAN
rs667254	TUBAL3	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr10:6553200-6571400	Weak transcription	Pancreas	Pancrea
3	chr10:6557400-6582400	Weak transcription	Dnd41	blood
4	chr10:6558800-6579400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr10:6561200-6568400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:6561600-6568200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:6561600-6570400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:6561800-6564800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr10:6562200-6565000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:6562600-6566000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:6562600-6572200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:6562800-6580000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:6563000-6566600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr10:6563000-6579200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr10:6563200-6566000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:6563200-6566000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr10:6563200-6566400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:6563200-6568200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:6563400-6565000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr10:6563400-6565600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr10:6563400-6567600	Weak transcription	K562	blood
22	chr10:6563400-6568400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr10:6563400-6568600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:6563800-6565200	Weak transcription	Fetal Thymus	thymus
25	chr10:6563800-6566600	Weak transcription	Thymus	Thymus
26	chr10:6563800-6567000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:6563800-6567600	Weak transcription	Primary T cells from cord blood	blood
28	chr10:6564000-6566400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:6564400-6565000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr10:6564400-6565400	Weak transcription	Primary T cells fromperipheralblood	blood

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