Variant report

Variant	rs4847257
Chromosome Location	chr1:94219686-94219687
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	chr1:94213369..94215810-chr1:94218586..94221367,2	MCF-7	breast:
2	chr1:94145323..94148892-chr1:94219465..94224318,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNTTIP2-1	chr1:94218480-94219902	ENSG00000230439
2	lnc-DNTTIP2-1	chr1:94217335-94219902	NONHSAT004544

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10874797	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11164970	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164973	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11164974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165022	0.82[CEU][hapmap]
rs11582870	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1884019	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs1980083	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs2092700	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2391315	0.85[CEU][hapmap]
rs2391321	0.85[CEU][hapmap]
rs2747036	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747037	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747038	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747040	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2747044	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2747047	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2747049	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2818161	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2818165	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818166	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818167	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3789453	0.83[GIH][hapmap]
rs4520428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847184	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847192	0.90[EUR][1000 genomes]
rs4847254	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6541399	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6660210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6667986	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6681265	0.81[CEU][hapmap]
rs6703684	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs743110	0.86[GIH][hapmap]
rs7523787	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7552293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs947343	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9651128	0.88[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4847257	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs4847257	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs4847257	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4847257	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs4847257	RP11-488P3.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94215600-94220000	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr1:94215600-94220600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:94215800-94220200	Enhancers	Fetal Lung	lung
4	chr1:94216000-94224800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:94216200-94219800	Enhancers	Psoas Muscle	Psoas
6	chr1:94216200-94219800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:94216200-94220000	Genic enhancers	HMEC	breast
8	chr1:94216400-94223800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:94216600-94220600	Enhancers	Placenta	Placenta
10	chr1:94216800-94221200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:94216800-94223000	Enhancers	Osteobl	bone
12	chr1:94216800-94224400	Weak transcription	Right Atrium	heart
13	chr1:94217200-94221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:94217400-94220600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:94217600-94223200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:94218000-94220000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr1:94218000-94222400	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:94218000-94222600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:94218000-94222800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:94218000-94223200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:94218000-94223800	Weak transcription	Thymus	Thymus
22	chr1:94218000-94224200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:94218400-94222200	Weak transcription	Left Ventricle	heart
24	chr1:94218400-94222600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:94218400-94222800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:94218400-94222800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:94218600-94220600	Enhancers	HepG2	liver
28	chr1:94218600-94222600	Enhancers	NHDF-Ad	bronchial
29	chr1:94218800-94220600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:94218800-94222600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:94218800-94223600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:94218800-94225200	Enhancers	NHLF	lung
33	chr1:94219000-94220800	Enhancers	HUVEC	blood vessel
34	chr1:94219000-94221800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:94219000-94221800	Enhancers	NHEK	skin
36	chr1:94219200-94219800	Enhancers	Brain Hippocampus Middle	brain
37	chr1:94219200-94219800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:94219200-94220000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:94219200-94220000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:94219200-94220600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:94219200-94220600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:94219200-94220800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:94219400-94219800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:94219400-94219800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:94219400-94219800	Enhancers	Right Ventricle	heart
46	chr1:94219400-94219800	Flanking Active TSS	Hela-S3	cervix
47	chr1:94219400-94219800	Flanking Active TSS	HSMM	muscle
48	chr1:94219400-94220000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:94219400-94220000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:94219400-94220000	Enhancers	Aorta	Aorta

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