Variant report

Variant	rs2581801
Chromosome Location	chr3:52972907-52972908
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52969267..52971322-chr3:52971385..52973436,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11130332	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1134546	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs11706243	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11707576	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708223	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082061	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13083728	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1573815	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs17304995	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2245424	0.86[JPT][hapmap]
rs2246556	0.83[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255107	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2257216	0.86[JPT][hapmap]
rs2276817	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs2276825	0.94[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap]
rs2336162	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2336666	0.85[EUR][1000 genomes]
rs2336669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2336670	0.85[JPT][hapmap]
rs2336671	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2439434	0.81[ASN][1000 genomes]
rs2465101	0.81[ASN][1000 genomes]
rs2564947	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2581779	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2581796	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581797	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2581802	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581803	0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2581805	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2581810	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581815	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2581820	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2581823	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2710313	0.81[ASN][1000 genomes]
rs2710314	0.86[JPT][hapmap]
rs2710342	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2710345	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34230854	0.88[EUR][1000 genomes]
rs35380116	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733047	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4302374	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs4519686	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687554	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4687559	0.85[EUR][1000 genomes]
rs4687560	0.85[EUR][1000 genomes]
rs4687658	0.81[CEU][hapmap]
rs4687663	0.81[CEU][hapmap]
rs4687672	0.80[CEU][hapmap]
rs4687692	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59989280	0.86[EUR][1000 genomes]
rs6445538	0.81[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs6445539	0.81[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs6445547	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs6445550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6768844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770957	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771610	0.83[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773040	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6789219	0.86[EUR][1000 genomes]
rs6792578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6797399	0.83[EUR][1000 genomes]
rs6803519	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs6805298	0.86[EUR][1000 genomes]
rs71301803	0.88[EUR][1000 genomes]
rs71301807	0.89[EUR][1000 genomes]
rs7621939	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637082	0.81[EUR][1000 genomes]
rs7644973	0.89[EUR][1000 genomes]
rs7648514	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]
rs7652131	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9311485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9682464	0.93[CEU][hapmap]
rs9812543	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9813024	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9823697	0.86[JPT][hapmap]
rs9825679	0.92[ASN][1000 genomes]
rs9828491	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9831409	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9836178	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9839035	0.83[EUR][1000 genomes]
rs9842974	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9844736	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9846976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847024	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9865094	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs9876403	0.94[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2581801	ITIH4-AS1	cis	lung	GTEx
rs2581801	ITIH4	cis	parietal	SCAN
rs2581801	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2581801	PPM1M	cis	parietal	SCAN
rs2581801	RFT1	cis	cerebellum	SCAN
rs2581801	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2581801	MUSTN1	cis	Artery Aorta	GTEx
rs2581801	GNL3	cis	cerebellum	SCAN
rs2581801	ITIH4	cis	cerebellum	SCAN
rs2581801	SEMA3G	cis	parietal	SCAN
rs2581801	WDR6	cis	cerebellum	SCAN
rs2581801	ITIH4	cis	lymphoblastoid	seeQTL
rs2581801	SERBP1P3	cis	lung	GTEx
rs2581801	GNL3	cis	parietal	SCAN
rs2581801	TMEM110	cis	cerebellum	SCAN
rs2581801	AMT	cis	parietal	SCAN
rs2581801	TMEM110	cis	parietal	SCAN
rs2581801	CHDH	cis	parietal	SCAN
rs2581801	NEK4	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:52941800-52980200	Weak transcription	Psoas Muscle	Psoas
3	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
4	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
5	chr3:52954800-52976800	Weak transcription	Brain Germinal Matrix	brain
6	chr3:52955200-52986400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:52956000-52973800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:52956400-52986400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:52957200-52974800	Weak transcription	Primary T cells from cord blood	blood
10	chr3:52958200-52985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:52960200-52979600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:52961600-52987000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52962400-52975800	Weak transcription	HepG2	liver
14	chr3:52962400-52986600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:52962400-52998200	Weak transcription	Lung	lung
16	chr3:52962400-53001600	Weak transcription	Brain Angular Gyrus	brain
17	chr3:52962400-53007000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:52962600-52979400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:52963000-52974800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:52963000-52976400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:52964200-52975600	Weak transcription	Fetal Intestine Small	intestine
23	chr3:52964200-52984400	Weak transcription	Fetal Stomach	stomach
24	chr3:52964200-52995400	Weak transcription	Gastric	stomach
25	chr3:52964400-52976000	Weak transcription	Fetal Intestine Large	intestine
26	chr3:52964400-52984200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:52964400-52988200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:52965000-52973600	Weak transcription	Hela-S3	cervix
30	chr3:52965000-52976600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:52965000-52986000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:52965000-52986800	Weak transcription	Thymus	Thymus
33	chr3:52965000-52998400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
35	chr3:52965200-52976800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:52965200-52986600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:52965400-52973600	Weak transcription	Primary B cells from cord blood	blood
38	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
39	chr3:52966200-52976600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:52966200-52985800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr3:52966400-52973000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:52966400-52976800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52966400-52986000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:52966400-52986200	Weak transcription	Placenta	Placenta
45	chr3:52966400-53001600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:52968800-52986400	Weak transcription	Fetal Thymus	thymus
47	chr3:52969000-52973200	Weak transcription	A549	lung
48	chr3:52969000-52986400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:52969200-52986400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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