Variant report

Variant	rs10159978
Chromosome Location	chr10:27103056-27103057
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	chr10:27093725..27095601-chr10:27102289..27104640,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10764642	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10764644	0.93[AFR][1000 genomes]
rs10764645	0.85[AFR][1000 genomes]
rs10764654	0.81[AFR][1000 genomes]
rs10829055	0.86[YRI][hapmap]
rs10829056	0.86[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10829057	0.88[AFR][1000 genomes]
rs10829059	0.93[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs10829061	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10829062	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]
rs10829068	0.93[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829069	0.80[ASW][hapmap];0.93[CEU][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829072	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10829073	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829074	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829076	0.82[AFR][1000 genomes]
rs10829077	0.84[YRI][hapmap]
rs10829079	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829083	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829085	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10829088	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829099	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs10829103	0.81[AFR][1000 genomes]
rs10829107	0.85[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11015262	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11015266	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11015267	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015276	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11015283	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11015298	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11015300	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015308	0.86[EUR][1000 genomes]
rs11015313	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015340	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11015343	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1115707	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12243481	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12247684	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12256219	0.92[AFR][1000 genomes]
rs12265625	0.85[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12267091	0.93[AFR][1000 genomes]
rs12358409	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1408530	0.93[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs16927341	0.85[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17754383	0.88[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs17754419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17754431	0.88[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs17816551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17816804	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs28538332	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4628582	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs55806416	0.86[ASN][1000 genomes]
rs7082503	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7097837	0.83[YRI][hapmap]
rs718827	0.93[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72629717	0.89[ASN][1000 genomes]
rs72629724	0.98[ASN][1000 genomes]
rs72629725	0.98[ASN][1000 genomes]
rs72629726	0.98[ASN][1000 genomes]
rs72629727	0.98[ASN][1000 genomes]
rs72629728	0.98[ASN][1000 genomes]
rs72629729	0.82[ASN][1000 genomes]
rs72629730	0.98[ASN][1000 genomes]
rs72629731	1.00[ASN][1000 genomes]
rs72629733	0.97[ASN][1000 genomes]
rs72629734	0.99[ASN][1000 genomes]
rs72629738	0.90[ASN][1000 genomes]
rs7894246	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7910026	0.89[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs899372	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs899373	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10159978	HRG	trans	cerebellum	SCAN
rs10159978	ABI1	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27075000-27104600	Weak transcription	Esophagus	oesophagus
2	chr10:27082200-27105400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:27085600-27119000	Weak transcription	Fetal Lung	lung
4	chr10:27086600-27110400	Weak transcription	Fetal Intestine Large	intestine
5	chr10:27091800-27113200	Weak transcription	Placenta	Placenta
6	chr10:27093400-27112400	Weak transcription	Left Ventricle	heart
7	chr10:27094000-27108000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:27094600-27108400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:27094600-27111200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr10:27094800-27104400	Weak transcription	Psoas Muscle	Psoas
11	chr10:27094800-27108000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:27094800-27111200	Weak transcription	Ovary	ovary
13	chr10:27095000-27130600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr10:27095000-27138600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr10:27095200-27105000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:27095200-27106600	Weak transcription	Osteobl	bone
17	chr10:27095200-27110800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr10:27095200-27119000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:27095400-27104400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr10:27095400-27110800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr10:27095400-27111200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:27095400-27113000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr10:27095400-27116200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:27095400-27129800	Weak transcription	NHEK	skin
25	chr10:27095600-27103400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:27095600-27105000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:27095600-27105800	Weak transcription	Lung	lung
28	chr10:27095600-27105800	Weak transcription	Thymus	Thymus
29	chr10:27095600-27106000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:27095600-27106000	Weak transcription	Aorta	Aorta
31	chr10:27095600-27107800	Weak transcription	Brain Hippocampus Middle	brain
32	chr10:27095600-27109800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr10:27095600-27111000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:27095600-27114600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr10:27095600-27115400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr10:27095600-27129000	Weak transcription	Right Atrium	heart
37	chr10:27095600-27132600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr10:27095600-27148800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr10:27095800-27113400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr10:27096600-27106200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr10:27096800-27104600	Weak transcription	Small Intestine	intestine
42	chr10:27096800-27105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:27096800-27106000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:27096800-27108200	Weak transcription	Brain Substantia Nigra	brain
45	chr10:27096800-27108200	Weak transcription	Fetal Thymus	thymus
46	chr10:27096800-27110800	Weak transcription	Dnd41	blood
47	chr10:27096800-27112400	Weak transcription	Gastric	stomach
48	chr10:27097000-27104800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr10:27097000-27104800	Weak transcription	GM12878-XiMat	blood
50	chr10:27097200-27103200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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