Variant report

Variant	rs3951780
Chromosome Location	chr10:22062729-22062730
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:22052432..22054490-chr10:22062596..22064322,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10508639	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs10740991	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs10828264	1.00[CHB][hapmap];0.82[MKK][hapmap]
rs10828266	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap]
rs11012794	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs12356674	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs1243180	0.85[CEU][hapmap]
rs1243194	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap]
rs1243195	1.00[CHB][hapmap]
rs1269454	1.00[CHB][hapmap]
rs2026092	1.00[CHB][hapmap]
rs2050905	0.85[MKK][hapmap]
rs2066270	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2066271	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2666754	1.00[ASW][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap]
rs2666757	1.00[ASW][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap]
rs2666759	0.89[CEU][hapmap]
rs2666768	0.90[CEU][hapmap]
rs2666769	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2666771	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap]
rs2666772	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs2666775	0.90[CEU][hapmap];0.84[GIH][hapmap]
rs2666776	1.00[ASW][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap]
rs2666779	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2666782	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2807968	1.00[ASW][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap]
rs2807971	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap]
rs2807977	1.00[CHB][hapmap]
rs2807979	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs2807984	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap]
rs2807985	0.89[ASW][hapmap];0.85[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs2807986	0.84[CEU][hapmap]
rs2807987	1.00[ASW][hapmap];0.90[CEU][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs2998360	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap]
rs4024198	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap]
rs6482190	0.84[AMR][1000 genomes]
rs7082663	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap]
rs792453	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs792455	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs806774	0.85[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052464	chr10:21856531-22220087	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv1802317	chr10:21866085-22288132	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv894947	chr10:21869609-22117913	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv550203	chr10:21916468-22062729	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv540513	chr10:22031022-22065456	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv3366640	chr10:22061996-22064094	Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3951780	MLLT10	Cis_1M	lymphoblastoid	RTeQTL
rs3951780	PXDN	trans	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22034400-22074000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:22036200-22066600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:22047200-22074000	Weak transcription	K562	blood
4	chr10:22048000-22109000	Weak transcription	Ovary	ovary
5	chr10:22048200-22069200	Weak transcription	Right Ventricle	heart
6	chr10:22048200-22074000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:22048400-22070400	Weak transcription	Pancreas	Pancrea
8	chr10:22048400-22087400	Weak transcription	Aorta	Aorta
9	chr10:22048400-22094800	Weak transcription	Small Intestine	intestine
10	chr10:22048400-22099200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:22048600-22067600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:22048600-22067800	Weak transcription	Lung	lung
13	chr10:22048600-22074000	Weak transcription	Left Ventricle	heart
14	chr10:22048600-22074000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:22048600-22076400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr10:22048600-22076600	Weak transcription	Gastric	stomach
17	chr10:22048800-22079600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr10:22048800-22114000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr10:22049000-22086400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:22049400-22074000	Weak transcription	Liver	Liver
21	chr10:22053200-22064800	Weak transcription	Primary B cells from cord blood	blood
22	chr10:22054200-22076600	Weak transcription	Fetal Lung	lung
23	chr10:22054600-22066800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr10:22055200-22067800	Weak transcription	Fetal Stomach	stomach
25	chr10:22055400-22095600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:22061000-22065600	Weak transcription	Primary T cells from cord blood	blood
27	chr10:22061000-22065600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr10:22061000-22066200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr10:22061000-22066400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr10:22061000-22066600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr10:22061000-22077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr10:22061200-22067000	Weak transcription	Stomach Mucosa	stomach
33	chr10:22061400-22063400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:22061600-22067600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:22061800-22064200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:22062000-22067200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr10:22062200-22067800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr10:22062200-22088800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:22062600-22067600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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