Variant report

Variant	rs1235000
Chromosome Location	chr1:114134025-114134026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10776773	0.80[ASN][1000 genomes]
rs10858003	0.83[ASN][1000 genomes]
rs10858006	0.96[ASN][1000 genomes]
rs11102667	0.88[ASN][1000 genomes]
rs11102678	0.81[ASW][hapmap];0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs1146183	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.90[ASN][1000 genomes]
rs1146184	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1146185	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[ASN][1000 genomes]
rs12026423	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.92[ASN][1000 genomes]
rs12138638	0.84[ASN][1000 genomes]
rs1217194	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1217202	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217212	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1217216	0.95[AFR][1000 genomes]
rs1217222	0.85[AFR][1000 genomes]
rs1217224	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217225	1.00[ASW][hapmap];0.94[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1217229	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217231	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1217238	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1230673	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.88[ASN][1000 genomes]
rs1230675	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1237290	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12757859	0.84[ASN][1000 genomes]
rs1343630	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs13524	0.86[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs1624335	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1743594	0.87[ASW][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1743595	0.90[ASN][1000 genomes]
rs1777239	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1935836	0.83[CEU][hapmap];0.85[CHB][hapmap];0.83[YRI][hapmap]
rs2040041	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs2636003	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2798137	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789597	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap]
rs7518766	0.92[ASN][1000 genomes]
rs7543121	0.86[ASN][1000 genomes]
rs9429525	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947311	chr1:114122533-114137619	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1235000	RAP1A	cis	parietal	SCAN
rs1235000	ADORA3	cis	parietal	SCAN
rs1235000	SIKE1	cis	parietal	SCAN
rs1235000	BCL2L15	cis	cerebellum	SCAN
rs1235000	AP4B1	cis	cerebellum	SCAN
rs1235000	PHTF1	cis	parietal	SCAN
rs1235000	MOV10	cis	cerebellum	SCAN
rs1235000	TRIM45	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114094800-114138400	Weak transcription	NHDF-Ad	bronchial
2	chr1:114100600-114140200	Weak transcription	Left Ventricle	heart
3	chr1:114100600-114173400	Weak transcription	Gastric	stomach
4	chr1:114110800-114139600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:114113000-114138400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:114116800-114138200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:114117600-114138400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:114118800-114136400	Weak transcription	Fetal Intestine Large	intestine
9	chr1:114119000-114140400	Weak transcription	Fetal Stomach	stomach
10	chr1:114119200-114138200	Weak transcription	Fetal Intestine Small	intestine
11	chr1:114119200-114140400	Weak transcription	Esophagus	oesophagus
12	chr1:114119200-114145200	Weak transcription	Lung	lung
13	chr1:114119200-114172400	Weak transcription	Pancreas	Pancrea
14	chr1:114119200-114173000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:114122400-114136600	Weak transcription	Fetal Lung	lung
16	chr1:114122400-114136800	Weak transcription	Placenta	Placenta
17	chr1:114122800-114137600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:114122800-114142600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:114123000-114136600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:114123000-114136800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:114123000-114138800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:114123400-114137600	Weak transcription	Dnd41	blood
23	chr1:114123400-114139600	Weak transcription	Fetal Heart	heart
24	chr1:114123600-114136800	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:114123800-114138400	Weak transcription	Small Intestine	intestine
26	chr1:114124200-114140200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:114124400-114172400	Weak transcription	Aorta	Aorta
28	chr1:114124600-114136400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:114124800-114139600	Weak transcription	Fetal Brain Male	brain
30	chr1:114125000-114136600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:114126600-114136600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:114126600-114139400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:114126600-114139400	Weak transcription	HSMM	muscle
34	chr1:114126600-114157200	Weak transcription	HUVEC	blood vessel
35	chr1:114126800-114138200	Weak transcription	Fetal Kidney	kidney
36	chr1:114127000-114136400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:114127000-114137600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:114127000-114139600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:114127200-114137200	Weak transcription	Adipose Nuclei	Adipose
40	chr1:114127400-114136600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:114127400-114139400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:114128000-114137000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:114128000-114139600	Weak transcription	HepG2	liver
44	chr1:114128000-114140000	Weak transcription	Ovary	ovary
45	chr1:114128200-114136800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:114128600-114136600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:114129200-114138600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:114131000-114136200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:114131800-114137600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:114132400-114138800	Weak transcription	Primary T cells from cord blood	blood

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