Variant report

Variant	rs17125278
Chromosome Location	chr10:91402877-91402878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:91402369..91405488-chr10:91459565..91463449,8	K562	blood:
2	chr10:91371070..91374344-chr10:91402272..91406788,6	MCF-7	breast:
3	chr10:91369955..91372663-chr10:91402410..91404170,2	K562	blood:
4	chr10:91401983..91406312-chr10:91459063..91463449,10	K562	blood:
5	chr10:91402267..91405688-chr10:91407429..91411344,10	K562	blood:
6	chr10:91402561..91404356-chr12:56108835..56111046,2	MCF-7	breast:
7	chr10:91402715..91410625-chr10:91458897..91464646,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225836	Chromatin interaction
ENSG00000258311	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000152782	Chromatin interaction
ENSG00000235100	Chromatin interaction
ENSG00000138182	Chromatin interaction
ENSG00000135441	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10430645	0.93[CEU][hapmap]
rs10430646	0.88[CEU][hapmap]
rs1048057	0.93[CEU][hapmap]
rs10509579	0.93[CEU][hapmap]
rs1062465	0.93[CEU][hapmap]
rs10785893	0.85[AMR][1000 genomes]
rs10785894	0.85[AMR][1000 genomes]
rs10785895	0.85[AMR][1000 genomes]
rs10785896	0.94[CEU][hapmap];0.85[AMR][1000 genomes]
rs10881614	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10881615	0.85[AMR][1000 genomes]
rs10881618	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs10881619	0.94[CEU][hapmap];0.85[AMR][1000 genomes]
rs10881621	0.81[AMR][1000 genomes]
rs10881623	0.81[AMR][1000 genomes]
rs10881628	0.88[CEU][hapmap]
rs10881629	0.88[CEU][hapmap]
rs10881631	0.88[CEU][hapmap]
rs10881632	0.97[ASN][1000 genomes]
rs10881647	0.85[CEU][hapmap]
rs10881664	0.87[CEU][hapmap]
rs10881666	0.93[CEU][hapmap]
rs11185825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11185826	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11185830	0.85[AMR][1000 genomes]
rs11185831	0.85[AMR][1000 genomes]
rs11185833	0.85[AMR][1000 genomes]
rs11185861	0.88[CEU][hapmap]
rs11185867	0.92[ASN][1000 genomes]
rs11185879	0.87[ASN][1000 genomes]
rs11185880	0.84[CEU][hapmap]
rs11813204	0.97[ASN][1000 genomes]
rs11816741	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs12218194	0.87[AMR][1000 genomes]
rs12250365	0.93[CEU][hapmap]
rs12767644	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12769113	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12773740	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12773865	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12779880	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1409358	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs1555868	0.88[CEU][hapmap]
rs1886997	0.93[CEU][hapmap]
rs1887037	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2026550	0.88[CEU][hapmap]
rs2077946	0.87[CEU][hapmap]
rs2094212	0.80[AMR][1000 genomes]
rs2094213	0.85[AMR][1000 genomes]
rs2182396	0.88[CEU][hapmap]
rs35754486	0.87[ASN][1000 genomes]
rs36190073	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3740037	0.93[CEU][hapmap]
rs3758385	0.88[CEU][hapmap]
rs3824609	0.93[CEU][hapmap]
rs3908479	0.85[AMR][1000 genomes]
rs4558081	0.85[AMR][1000 genomes]
rs6586218	0.88[CEU][hapmap]
rs7070916	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7073779	0.85[AMR][1000 genomes]
rs7074093	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7076259	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7077349	0.88[CEU][hapmap]
rs7081362	0.88[CEU][hapmap]
rs7085805	0.88[CEU][hapmap]
rs7087240	0.94[CEU][hapmap];0.85[AMR][1000 genomes]
rs7087789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7088104	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs7088570	0.85[AMR][1000 genomes]
rs7089473	0.88[CEU][hapmap]
rs7092444	0.93[CEU][hapmap]
rs7094633	0.85[AMR][1000 genomes]
rs7095818	0.93[CEU][hapmap]
rs7096466	0.93[CEU][hapmap]
rs7096826	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7097496	0.94[CEU][hapmap];0.85[AMR][1000 genomes]
rs7100603	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs716781	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs727427	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7895379	0.93[CEU][hapmap]
rs7898670	0.87[CEU][hapmap]
rs7907852	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7909550	0.87[CEU][hapmap]
rs7912464	0.81[CEU][hapmap]
rs7914590	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8181361	0.93[CEU][hapmap]
rs8181406	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9325443	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs9325444	0.94[CEU][hapmap]
rs943129	0.84[AMR][1000 genomes]
rs962524	0.93[CEU][hapmap]
rs9663129	0.88[CEU][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17125278	LINC00865	cis	Artery Tibial	GTEx
rs17125278	LINC00865	cis	Nerve Tibial	GTEx
rs17125278	LINC00865	cis	lung	GTEx
rs17125278	RP11-248C1.3	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91351600-91403400	Weak transcription	Esophagus	oesophagus
2	chr10:91352600-91403400	Weak transcription	Small Intestine	intestine
3	chr10:91353800-91403800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:91359800-91403200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:91370200-91403200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:91371800-91403200	Weak transcription	HSMMtube	muscle
7	chr10:91380600-91403200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:91385000-91403000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:91385400-91403000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:91385800-91403200	Weak transcription	Fetal Brain Male	brain
11	chr10:91386000-91403000	Weak transcription	NHDF-Ad	bronchial
12	chr10:91386000-91403200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr10:91386000-91403200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:91386000-91403200	Weak transcription	Ovary	ovary
15	chr10:91386800-91403200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:91388200-91403400	Weak transcription	Thymus	Thymus
17	chr10:91392600-91403000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr10:91392600-91403200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:91392600-91403200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr10:91393000-91403200	Weak transcription	Fetal Thymus	thymus
21	chr10:91393800-91403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:91394200-91403000	Weak transcription	Fetal Brain Female	brain
23	chr10:91394400-91403200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:91394800-91403000	Weak transcription	Brain Hippocampus Middle	brain
25	chr10:91394800-91403200	Weak transcription	HSMM	muscle
26	chr10:91395400-91403800	Weak transcription	Lung	lung
27	chr10:91396000-91403000	Weak transcription	Primary T cells from cord blood	blood
28	chr10:91396000-91403800	Weak transcription	Spleen	Spleen
29	chr10:91396400-91403200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:91397000-91403200	Weak transcription	Fetal Stomach	stomach
31	chr10:91397200-91403000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr10:91397600-91403000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr10:91398200-91403000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:91399400-91403000	Enhancers	Fetal Intestine Large	intestine
35	chr10:91399600-91403000	Enhancers	Fetal Heart	heart
36	chr10:91399600-91403400	Weak transcription	Left Ventricle	heart
37	chr10:91399800-91403000	Weak transcription	Right Atrium	heart
38	chr10:91400200-91403200	Weak transcription	Brain Anterior Caudate	brain
39	chr10:91401000-91403000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:91401000-91405200	Active TSS	GM12878-XiMat	blood
41	chr10:91401200-91403000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:91401600-91403000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr10:91401600-91403000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr10:91401600-91403000	Enhancers	Hela-S3	cervix
45	chr10:91401600-91403200	Enhancers	Fetal Lung	lung
46	chr10:91401600-91405200	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr10:91401600-91405400	Active TSS	Fetal Kidney	kidney
48	chr10:91401800-91403800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr10:91402000-91403200	Active TSS	Duodenum Mucosa	Duodenum
50	chr10:91402000-91403600	Flanking Active TSS	Dnd41	blood

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