Variant report

Variant	rs4838993
Chromosome Location	chr1:114135133-114135134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12144215	0.87[ASN][1000 genomes]
rs1217225	0.81[CHD][hapmap]
rs1419231	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17274627	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17359281	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17359378	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17359468	0.80[ASN][1000 genomes]
rs17461918	0.86[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17508449	0.86[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2146018	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3761934	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41352847	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4838994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4839000	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4839327	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4839329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4839331	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4839332	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4839333	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs4839336	0.90[ASN][1000 genomes]
rs6678422	0.92[ASN][1000 genomes]
rs7514649	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1012324	chr1:114135133-114206843	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4838993	KCNA10	cis	parietal	SCAN
rs4838993	ADORA3	cis	parietal	SCAN
rs4838993	PTPN22	cis	multi-tissue	Pritchard
rs4838993	PHTF1	cis	lymphoblastoid	seeQTL
rs4838993	CD53	cis	parietal	SCAN

Chromatin state (count:55 , 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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