Variant report

Variant	rs7648514
Chromosome Location	chr3:52983246-52983247
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11130332	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1134546	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11706243	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11707576	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11708223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082061	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083728	0.82[CEU][hapmap]
rs1573815	0.82[CEU][hapmap]
rs17304995	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2245424	0.89[JPT][hapmap]
rs2246556	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2255107	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2257216	0.89[JPT][hapmap]
rs2276817	0.82[CEU][hapmap]
rs2276825	0.94[CEU][hapmap]
rs2336162	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2336666	0.83[EUR][1000 genomes]
rs2336669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2336670	0.88[JPT][hapmap]
rs2336671	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2564947	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2581779	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2581780	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2581796	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581797	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2581801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581802	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581803	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2581805	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2581810	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2581815	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581820	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581823	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2710314	0.89[JPT][hapmap]
rs2710342	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2710345	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34230854	0.86[EUR][1000 genomes]
rs35380116	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733047	0.82[CEU][hapmap]
rs4302374	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs4519686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687554	0.82[CEU][hapmap]
rs4687559	0.83[EUR][1000 genomes]
rs4687560	0.83[EUR][1000 genomes]
rs4687692	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59989280	0.84[EUR][1000 genomes]
rs6445538	0.82[CEU][hapmap]
rs6445539	0.82[CEU][hapmap]
rs6445547	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs6445550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6768844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770957	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771610	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6773040	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6789219	0.84[EUR][1000 genomes]
rs6792578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6797399	0.81[EUR][1000 genomes]
rs6803519	0.82[CEU][hapmap]
rs6805298	0.84[EUR][1000 genomes]
rs71301803	0.86[EUR][1000 genomes]
rs71301807	0.87[EUR][1000 genomes]
rs7621939	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7644973	0.87[EUR][1000 genomes]
rs7652131	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311485	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9682464	0.88[CEU][hapmap]
rs9812543	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9813024	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9823697	0.89[JPT][hapmap]
rs9825679	0.90[ASN][1000 genomes]
rs9828491	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9831409	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9839035	0.81[EUR][1000 genomes]
rs9842974	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9844736	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9846976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847024	0.91[EUR][1000 genomes]
rs9865094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9876403	0.94[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7648514	ITIH4-AS1	cis	lung	GTEx
rs7648514	SERBP1P3	cis	lung	GTEx
rs7648514	ITIH4-AS1	cis	Artery Aorta	GTEx
rs7648514	ITIH4-AS1	cis	Artery Tibial	GTEx
rs7648514	MUSTN1	cis	Artery Aorta	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
2	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
3	chr3:52955200-52986400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:52956400-52986400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:52958200-52985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:52961600-52987000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:52962400-52986600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:52962400-52998200	Weak transcription	Lung	lung
9	chr3:52962400-53001600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:52962400-53007000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
12	chr3:52964200-52984400	Weak transcription	Fetal Stomach	stomach
13	chr3:52964200-52995400	Weak transcription	Gastric	stomach
14	chr3:52964400-52984200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:52964400-52988200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:52965000-52986000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:52965000-52986800	Weak transcription	Thymus	Thymus
19	chr3:52965000-52998400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
21	chr3:52965200-52986600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
23	chr3:52966200-52985800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:52966400-52986000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:52966400-52986200	Weak transcription	Placenta	Placenta
26	chr3:52966400-53001600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:52968800-52986400	Weak transcription	Fetal Thymus	thymus
28	chr3:52969000-52986400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:52969200-52986400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:52969200-52991000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:52969200-52996200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:52969200-52997400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:52969400-52986600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:52972400-52986400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:52975000-53008000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:52975200-52986000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:52975200-52986400	Weak transcription	Primary T cells from cord blood	blood
39	chr3:52975200-53000600	Weak transcription	Hela-S3	cervix
40	chr3:52976400-52986400	Weak transcription	Primary B cells from cord blood	blood
41	chr3:52977000-52987000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:52977400-52986000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:52977400-52986000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:52977600-52985800	Weak transcription	Fetal Intestine Large	intestine
45	chr3:52977600-52986000	Weak transcription	Liver	Liver
46	chr3:52977600-52986400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:52977600-52986400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:52977800-52986000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:52977800-52986000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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