Variant report

Variant	rs10828258
Chromosome Location	chr10:21929734-21929735
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	chr10:21784438..21784982-chr10:21929257..21929911,2	K562	blood:
2	chr10:21909889..21911580-chr10:21929468..21932103,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10430587	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10508639	1.00[YRI][hapmap]
rs10740991	1.00[YRI][hapmap]
rs10828247	0.80[TSI][hapmap]
rs10828248	0.82[TSI][hapmap]
rs10828249	0.82[TSI][hapmap]
rs10828252	0.87[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.85[AFR][1000 genomes]
rs10828256	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10828264	0.85[GIH][hapmap]
rs10828266	0.82[MEX][hapmap]
rs11012737	0.87[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.85[AFR][1000 genomes]
rs11012750	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11012794	1.00[ASW][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs11592565	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12356674	0.87[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.85[AFR][1000 genomes]
rs1243179	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1243180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1243182	1.00[JPT][hapmap]
rs1243184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1243185	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1243187	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1243188	0.82[ASN][1000 genomes]
rs1243189	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1243192	0.82[AMR][1000 genomes]
rs1243194	0.91[GIH][hapmap]
rs1269454	0.86[CEU][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1270799	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12769128	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12770228	0.87[ASW][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap]
rs12783517	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2026092	0.82[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2050905	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap]
rs35587371	0.81[EUR][1000 genomes]
rs3951780	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs4748761	0.81[AMR][1000 genomes]
rs7082663	1.00[ASW][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs7090708	0.88[EUR][1000 genomes]
rs7098100	0.82[TSI][hapmap]
rs946711	0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036585	chr10:21833717-21998042	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv550202	chr10:21856475-22027644	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv1792771	chr10:21874152-22013644	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	esv1803077	chr10:21878144-22013644	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10828258	MLLT10	Cis_1M	lymphoblastoid	RTeQTL
rs10828258	PSTPIP2	trans	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:21824600-21930400	Weak transcription	Gastric	stomach
2	chr10:21874000-21938400	Weak transcription	Spleen	Spleen
3	chr10:21896800-21973200	Weak transcription	Hela-S3	cervix
4	chr10:21897400-21960200	Weak transcription	Fetal Brain Male	brain
5	chr10:21898200-21941200	Weak transcription	Fetal Kidney	kidney
6	chr10:21898600-21943800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:21899400-21938000	Weak transcription	Aorta	Aorta
8	chr10:21901000-21933600	Weak transcription	Right Ventricle	heart
9	chr10:21905400-21932200	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:21906600-21940600	Weak transcription	NH-A	brain
11	chr10:21908400-21964000	Weak transcription	Colonic Mucosa	Colon
12	chr10:21909400-21938200	Weak transcription	NHDF-Ad	bronchial
13	chr10:21913200-21947000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr10:21914000-21937600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr10:21914800-21937600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr10:21914800-21941800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr10:21915200-21938000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr10:21915200-21938200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:21915200-21938200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr10:21915200-21954200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr10:21915200-21983800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr10:21915400-21930400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:21915400-21933200	Weak transcription	Left Ventricle	heart
24	chr10:21915400-21967000	Weak transcription	Pancreas	Pancrea
25	chr10:21915800-21941000	Weak transcription	Osteobl	bone
26	chr10:21916600-21938400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:21916800-21950200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr10:21917200-21967400	Weak transcription	Brain Angular Gyrus	brain
29	chr10:21917400-21933000	Weak transcription	Fetal Heart	heart
30	chr10:21917400-21938400	Weak transcription	HMEC	breast
31	chr10:21917400-21940800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:21917600-21944600	Weak transcription	Ovary	ovary
33	chr10:21918600-21938200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr10:21919800-21938200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:21920000-21932400	Weak transcription	Fetal Lung	lung
36	chr10:21920000-21938200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr10:21920000-21965600	Weak transcription	Esophagus	oesophagus
38	chr10:21920800-21939800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:21922400-21929800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:21922400-21930000	Strong transcription	Fetal Thymus	thymus
41	chr10:21923000-21929800	Strong transcription	K562	blood
42	chr10:21923400-21931200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:21923600-21931400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr10:21923800-21983200	Weak transcription	NHLF	lung
45	chr10:21924000-21931200	Strong transcription	Fetal Intestine Large	intestine
46	chr10:21924000-21941200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr10:21924200-21936200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr10:21924200-21942000	Weak transcription	Small Intestine	intestine
49	chr10:21924200-21944600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr10:21924200-21962400	Weak transcription	HSMM	muscle

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