Variant report

Variant	rs10829062
Chromosome Location	chr10:27066379-27066380
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:27050958..27053361-chr10:27064664..27066891,2	K562	blood:
2	chr10:27061393..27062937-chr10:27066179..27068006,2	MCF-7	breast:
3	chr10:27064202..27066612-chr10:27068536..27071634,3	K562	blood:
4	chr10:27066132..27067920-chr10:27074183..27076184,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10159978	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10764642	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10764644	0.90[AFR][1000 genomes]
rs10764645	0.83[AFR][1000 genomes]
rs10829055	0.86[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10829056	0.93[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10829057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10829059	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10829061	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10829068	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10829069	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10829072	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829073	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10829074	0.93[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10829077	0.84[YRI][hapmap]
rs10829079	0.91[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10829083	0.81[EUR][1000 genomes]
rs10829085	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10829088	0.81[EUR][1000 genomes]
rs10829099	0.91[YRI][hapmap]
rs10829107	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11015262	1.00[ASW][hapmap];0.86[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11015266	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11015267	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11015276	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11015283	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11015298	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015300	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11015308	0.95[EUR][1000 genomes]
rs11015313	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11015340	0.94[EUR][1000 genomes]
rs11015343	0.96[EUR][1000 genomes]
rs12243481	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12247684	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12256219	0.85[AFR][1000 genomes]
rs12265625	0.92[CEU][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12267091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12358409	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1408530	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16927341	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28538332	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7082503	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7097837	0.83[YRI][hapmap]
rs718827	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv933544	chr10:27005220-27111998	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers 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
3	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv6132	chr10:27066081-27075522	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10829062	HRG	trans	cerebellum	SCAN
rs10829062	ABI1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26988000-27069600	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:27021600-27069600	Weak transcription	Esophagus	oesophagus
3	chr10:27023400-27070000	Weak transcription	Pancreas	Pancrea
4	chr10:27025600-27069600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:27025800-27068200	Weak transcription	Spleen	Spleen
6	chr10:27025800-27070800	Weak transcription	Aorta	Aorta
7	chr10:27026000-27069600	Weak transcription	Brain Angular Gyrus	brain
8	chr10:27027400-27069400	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:27027800-27069600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:27028200-27068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:27028400-27069800	Weak transcription	NHLF	lung
12	chr10:27029800-27069600	Weak transcription	HSMMtube	muscle
13	chr10:27032000-27068200	Weak transcription	Small Intestine	intestine
14	chr10:27032000-27069600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:27032400-27069400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr10:27032400-27069600	Weak transcription	Lung	lung
17	chr10:27032600-27069800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:27033600-27069200	Weak transcription	Psoas Muscle	Psoas
19	chr10:27034000-27069000	Weak transcription	Colonic Mucosa	Colon
20	chr10:27034000-27069600	Weak transcription	Ovary	ovary
21	chr10:27034000-27069800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:27034400-27069600	Weak transcription	Right Ventricle	heart
23	chr10:27036800-27068400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:27044800-27068000	Weak transcription	K562	blood
25	chr10:27044800-27068400	Weak transcription	A549	lung
26	chr10:27044800-27069000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr10:27044800-27069600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr10:27044800-27070400	Weak transcription	HUVEC	blood vessel
29	chr10:27044800-27082000	Weak transcription	Fetal Lung	lung
30	chr10:27048200-27069400	Weak transcription	NHDF-Ad	bronchial
31	chr10:27051400-27082000	Weak transcription	Fetal Stomach	stomach
32	chr10:27054200-27066800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:27054400-27068400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:27054600-27068400	Weak transcription	Thymus	Thymus
35	chr10:27054800-27067400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr10:27054800-27069000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr10:27055400-27069000	Weak transcription	HSMM	muscle
38	chr10:27055600-27070200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr10:27056600-27067000	Weak transcription	GM12878-XiMat	blood
40	chr10:27056600-27068400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr10:27056600-27069200	Weak transcription	Placenta	Placenta
42	chr10:27057000-27067600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr10:27057200-27069600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:27057600-27068600	Weak transcription	Fetal Intestine Small	intestine
45	chr10:27057800-27067800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr10:27057800-27072000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr10:27058000-27067800	Weak transcription	Fetal Intestine Large	intestine
48	chr10:27058000-27067800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr10:27058000-27068200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr10:27058000-27072200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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