Variant report

Variant	rs10888385
Chromosome Location	chr1:150574302-150574303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150549850..150554291-chr1:150574089..150582135,21	MCF-7	breast:
2	chr1:150541344..150544160-chr1:150572544..150574410,2	K562	blood:
3	chr1:150548124..150553459-chr1:150571951..150579395,15	MCF-7	breast:
4	chr1:150532460..150535290-chr1:150572529..150575540,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203804	Chromatin interaction
ENSG00000264584	Chromatin interaction
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1053732	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888384	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204668	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11204669	0.88[ASN][1000 genomes]
rs11204675	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204677	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204678	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204679	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204680	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204684	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11585169	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12116492	0.81[ASN][1000 genomes]
rs12125672	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126271	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12139563	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12406712	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12746899	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1971378	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2048558	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738484	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3738485	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754209	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970918	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970923	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971041	0.85[ASN][1000 genomes]
rs55862611	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61820165	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669122	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6697620	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698495	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878471	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs932054	0.85[ASN][1000 genomes]
rs9803935	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv535157	chr1:150552692-150575941	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv946384	chr1:150567346-150579087	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs10888385	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs10888385	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs10888385	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs10888385	ARNT	cis	Thyroid	GTEx
rs10888385	ARNT	cis	Artery Aorta	GTEx
rs10888385	ENSA	Cis_1M	lymphoblastoid	RTeQTL
rs10888385	GOLPH3L	cis	Nerve Tibial	GTEx
rs10888385	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs10888385	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs10888385	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs10888385	HORMAD1	cis	Nerve Tibial	GTEx
rs10888385	RP11-316M1.12	cis	Whole Blood	GTEx
rs10888385	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs10888385	HORMAD1	cis	Esophagus Mucosa	GTEx
rs10888385	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs10888385	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553000-150583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:150553200-150577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:150553200-150581800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:150553200-150581800	Weak transcription	Dnd41	blood
5	chr1:150553200-150583200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
7	chr1:150553800-150576800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:150554000-150583200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:150555400-150582600	Weak transcription	Primary B cells from cord blood	blood
10	chr1:150560200-150576000	Weak transcription	Ovary	ovary
11	chr1:150561400-150577000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:150561800-150581800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:150562200-150583200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:150563000-150583800	Weak transcription	Fetal Lung	lung
15	chr1:150564000-150576200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:150564400-150583800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:150566200-150575800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:150566200-150575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:150566200-150576200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:150566400-150575800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:150566400-150583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:150566600-150577000	Weak transcription	Aorta	Aorta
23	chr1:150566800-150577000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:150568000-150583000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:150568200-150575400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:150568600-150576600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr1:150568600-150576800	Weak transcription	Spleen	Spleen
28	chr1:150568800-150575400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:150568800-150575800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:150568800-150575800	Weak transcription	Pancreas	Pancrea
31	chr1:150568800-150576200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:150568800-150576800	Weak transcription	Adipose Nuclei	Adipose
33	chr1:150569000-150576200	Weak transcription	Osteobl	bone
34	chr1:150569200-150582200	Weak transcription	Brain Anterior Caudate	brain
35	chr1:150569200-150582200	Weak transcription	GM12878-XiMat	blood
36	chr1:150569400-150576800	Weak transcription	Fetal Intestine Large	intestine
37	chr1:150569800-150575400	Weak transcription	Hela-S3	cervix
38	chr1:150569800-150575800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:150569800-150576600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:150569800-150576600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:150570000-150575800	Weak transcription	A549	lung
42	chr1:150570000-150575800	Weak transcription	K562	blood
43	chr1:150570000-150577200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:150570200-150576800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:150570400-150576800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:150570400-150582200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:150571000-150575800	Weak transcription	Left Ventricle	heart
48	chr1:150571000-150583800	Weak transcription	Primary T cells from cord blood	blood
49	chr1:150571400-150576800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:150571600-150574400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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