Variant report

Variant	rs17017399
Chromosome Location	chr1:211491340-211491341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210545971..210547559-chr1:211491010..211492840,2	MCF-7	breast:
2	chr1:211431679..211433826-chr1:211490845..211492829,2	K562	blood:
3	chr1:211461477..211464253-chr1:211490231..211493061,2	K562	blood:

Variant related genes	Relation type
ENSG00000117625	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11577985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11581989	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11582143	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11586974	0.92[YRI][hapmap]
rs11590228	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12041498	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs17017361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17017394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17017431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17017432	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17017441	0.83[LWK][hapmap]
rs17017451	0.85[CHD][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap]
rs34318448	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3767380	0.92[YRI][hapmap]
rs55654731	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55941941	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56380051	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61848978	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61848980	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61848982	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61850980	0.80[ASN][1000 genomes]
rs61851029	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61851030	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61851033	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6666324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7514863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7523875	1.00[CHD][hapmap]
rs7538100	0.85[CHD][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17017399	LINC00467	cis	Muscle Skeletal	GTEx
rs17017399	CTSE	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211461200-211499600	Weak transcription	Psoas Muscle	Psoas
2	chr1:211461400-211499600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:211461600-211499600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:211467200-211493800	Weak transcription	Fetal Brain Male	brain
5	chr1:211467800-211494200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:211474800-211497000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:211478600-211499800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:211479400-211492200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:211483600-211499600	Weak transcription	Fetal Heart	heart
10	chr1:211484600-211491600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:211486400-211499400	Weak transcription	Stomach Mucosa	stomach
12	chr1:211486400-211500200	Weak transcription	Small Intestine	intestine
13	chr1:211487200-211491400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:211487200-211492200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:211487200-211492800	Weak transcription	HepG2	liver
16	chr1:211487200-211496600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:211487200-211497000	Weak transcription	Fetal Stomach	stomach
18	chr1:211487200-211498800	Weak transcription	Thymus	Thymus
19	chr1:211487200-211499400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:211487200-211499600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:211487200-211499600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:211487200-211499600	Weak transcription	Brain Angular Gyrus	brain
23	chr1:211487200-211499600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:211487200-211499600	Weak transcription	Fetal Intestine Small	intestine
25	chr1:211487200-211499600	Weak transcription	Gastric	stomach
26	chr1:211487200-211499600	Weak transcription	Left Ventricle	heart
27	chr1:211487200-211499600	Weak transcription	Lung	lung
28	chr1:211487200-211499600	Weak transcription	Pancreas	Pancrea
29	chr1:211487200-211499800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:211487200-211499800	Weak transcription	Aorta	Aorta
31	chr1:211487200-211499800	Weak transcription	Esophagus	oesophagus
32	chr1:211487200-211499800	Weak transcription	Ovary	ovary
33	chr1:211487200-211499800	Weak transcription	Right Ventricle	heart
34	chr1:211487200-211500200	Weak transcription	Spleen	Spleen
35	chr1:211487400-211491600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:211487400-211499600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:211487400-211499600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:211487400-211499600	Weak transcription	Brain Anterior Caudate	brain
39	chr1:211487400-211499600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:211487400-211499600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:211487400-211499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:211487400-211499800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:211487400-211499800	Weak transcription	HSMMtube	muscle
44	chr1:211487600-211499600	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:211487600-211499600	Weak transcription	NHLF	lung
46	chr1:211488000-211499600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:211488000-211499600	Weak transcription	Brain Substantia Nigra	brain
48	chr1:211488200-211494200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:211488200-211496200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:211488200-211496800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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