Variant report

Variant	rs1398798
Chromosome Location	chr1:94199322-94199323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94146209..94148290-chr1:94198392..94201159,2	MCF-7	breast:
2	chr1:94199298..94200988-chr1:94312001..94313518,2	K562	blood:
3	chr1:94145431..94147694-chr1:94198446..94200278,2	MCF-7	breast:
4	chr1:94167250..94169551-chr1:94199187..94201792,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10489602	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs10489603	0.83[CEU][hapmap]
rs10489604	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs10782966	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10782967	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11165020	0.81[EUR][1000 genomes]
rs12122113	0.88[EUR][1000 genomes]
rs12134359	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12137687	0.88[EUR][1000 genomes]
rs12140446	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs12143274	0.88[EUR][1000 genomes]
rs12143279	0.88[EUR][1000 genomes]
rs12739186	0.81[EUR][1000 genomes]
rs12745990	0.88[EUR][1000 genomes]
rs1884018	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs2143990	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2235971	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs2391315	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2391322	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs2747039	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2747041	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2747043	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2747045	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2747050	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818160	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2818162	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2818164	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2818169	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3000471	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3747965	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs4075523	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4141737	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs4240955	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4240956	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4314890	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4350209	0.80[EUR][1000 genomes]
rs4847253	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6664719	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs6685747	0.87[EUR][1000 genomes]
rs8179391	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs871854	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1398798	RP11-488P3.1	cis	Artery Tibial	GTEx
rs1398798	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs1398798	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1398798	RP11-488P3.1	cis	Thyroid	GTEx
rs1398798	GCLM	Cis_1M	lymphoblastoid	RTeQTL
rs1398798	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs1398798	RP11-488P3.1	cis	lung	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94189000-94200000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:94190600-94200800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:94196200-94200600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:94196200-94205800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:94196600-94200000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:94196600-94204000	Weak transcription	Lung	lung
7	chr1:94197200-94199800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:94197400-94202000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:94197600-94200400	Weak transcription	HSMMtube	muscle
10	chr1:94197600-94200600	Weak transcription	Hela-S3	cervix
11	chr1:94197600-94201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:94197600-94205800	Weak transcription	Spleen	Spleen
13	chr1:94197800-94199400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:94197800-94199600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:94197800-94205800	Weak transcription	Right Atrium	heart
16	chr1:94198000-94199800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:94198000-94200400	Weak transcription	HMEC	breast
18	chr1:94198000-94200600	Weak transcription	NHEK	skin
19	chr1:94198000-94200800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:94198000-94201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:94198000-94202200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:94198200-94199400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:94198200-94199400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:94198200-94199400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:94198400-94200600	Weak transcription	A549	lung
26	chr1:94198400-94200800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:94198600-94199600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:94198600-94200800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:94198800-94200000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:94198800-94200600	Enhancers	Adipose Nuclei	Adipose
31	chr1:94199000-94199400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr1:94199000-94199400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:94199000-94199400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:94199000-94199400	Enhancers	HepG2	liver
35	chr1:94199000-94200600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:94199000-94204000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:94199000-94204000	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:94199000-94207000	Enhancers	HSMM	muscle
39	chr1:94199200-94199400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr1:94199200-94199400	Enhancers	Brain Angular Gyrus	brain
41	chr1:94199200-94199400	Enhancers	Right Ventricle	heart

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