Variant report

Variant	rs4350209
Chromosome Location	chr1:94217804-94217805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94216403..94218714-chr1:94221933..94224075,2	MCF-7	breast:
2	chr1:94146120..94148639-chr1:94215778..94219083,3	MCF-7	breast:
3	chr1:94210546..94213196-chr1:94216011..94218265,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10489602	0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs10489603	0.89[GIH][hapmap]
rs10489604	0.86[ASW][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs10782966	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10782967	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11165020	0.81[EUR][1000 genomes]
rs12122113	0.87[EUR][1000 genomes]
rs12134359	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12137687	0.87[EUR][1000 genomes]
rs12140446	0.86[ASW][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs12143274	0.87[EUR][1000 genomes]
rs12143279	0.87[EUR][1000 genomes]
rs12565817	0.89[GIH][hapmap]
rs12739186	0.80[EUR][1000 genomes]
rs12745990	0.87[EUR][1000 genomes]
rs1398798	0.80[EUR][1000 genomes]
rs2143990	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2235971	0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs2391322	0.93[GIH][hapmap];0.86[MEX][hapmap]
rs2747039	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2747041	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2747043	0.88[EUR][1000 genomes]
rs2747045	0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs2747050	0.87[EUR][1000 genomes]
rs2818160	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2818162	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2818164	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2818169	0.88[EUR][1000 genomes]
rs3000471	0.88[EUR][1000 genomes]
rs3747965	0.86[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs4075523	0.86[ASW][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4141737	0.86[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs4240955	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4240956	0.86[ASW][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4314890	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4847253	0.84[EUR][1000 genomes]
rs6664719	0.86[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs6685747	0.86[EUR][1000 genomes]
rs8179391	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs871854	0.84[EUR][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4350209	RP11-488P3.1	cis	lung	GTEx
rs4350209	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4350209	RP11-488P3.1	cis	Thyroid	GTEx
rs4350209	RP11-488P3.1	cis	Artery Tibial	GTEx
rs4350209	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs4350209	GCLM	Cis_1M	lymphoblastoid	RTeQTL
rs4350209	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs4350209	RP11-488P3.1	cis	Stomach	GTEx
rs4350209	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs4350209	RP11-488P3.1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94214400-94218000	Enhancers	Fetal Thymus	thymus
2	chr1:94215600-94218000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:94215600-94218000	Enhancers	Fetal Muscle Leg	muscle
4	chr1:94215600-94218000	Enhancers	Thymus	Thymus
5	chr1:94215600-94218200	Enhancers	Adipose Nuclei	Adipose
6	chr1:94215600-94218400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:94215600-94218400	Enhancers	Left Ventricle	heart
8	chr1:94215600-94218400	Enhancers	Right Ventricle	heart
9	chr1:94215600-94218800	Bivalent Enhancer	Fetal Heart	heart
10	chr1:94215600-94219200	Enhancers	Colon Smooth Muscle	Colon
11	chr1:94215600-94219400	Enhancers	Hela-S3	cervix
12	chr1:94215600-94220000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:94215600-94220600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:94215800-94218000	Enhancers	Lung	lung
15	chr1:94215800-94218400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:94215800-94220200	Enhancers	Fetal Lung	lung
17	chr1:94216000-94224800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:94216200-94218000	Enhancers	Esophagus	oesophagus
19	chr1:94216200-94218000	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:94216200-94218800	Weak transcription	A549	lung
21	chr1:94216200-94219800	Enhancers	Psoas Muscle	Psoas
22	chr1:94216200-94219800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:94216200-94220000	Genic enhancers	HMEC	breast
24	chr1:94216400-94219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:94216400-94219400	Enhancers	HSMM	muscle
26	chr1:94216400-94223800	Weak transcription	Fetal Intestine Small	intestine
27	chr1:94216600-94218000	Enhancers	Brain Anterior Caudate	brain
28	chr1:94216600-94218000	Enhancers	Brain Hippocampus Middle	brain
29	chr1:94216600-94218200	Enhancers	HSMMtube	muscle
30	chr1:94216600-94218400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:94216600-94218400	Enhancers	Rectal Smooth Muscle	rectum
32	chr1:94216600-94220600	Enhancers	Placenta	Placenta
33	chr1:94216800-94218000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:94216800-94219000	Weak transcription	HUVEC	blood vessel
35	chr1:94216800-94219400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:94216800-94221200	Weak transcription	Fetal Intestine Large	intestine
37	chr1:94216800-94223000	Enhancers	Osteobl	bone
38	chr1:94216800-94224400	Weak transcription	Right Atrium	heart
39	chr1:94217000-94218000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:94217000-94218000	Enhancers	Brain Angular Gyrus	brain
41	chr1:94217000-94218000	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:94217200-94218000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:94217200-94218000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:94217200-94218000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:94217200-94218200	Enhancers	NHDF-Ad	bronchial
46	chr1:94217200-94218400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:94217200-94218600	Weak transcription	HepG2	liver
48	chr1:94217200-94219600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:94217200-94221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:94217400-94218000	Enhancers	Brain Germinal Matrix	brain

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