Variant report

Variant	rs2336672
Chromosome Location	chr3:53007803-53007804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53004813..53006485-chr3:53007030..53009652,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11130332	0.80[ASN][1000 genomes]
rs2245424	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2257216	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2336670	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439434	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465101	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2564930	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581803	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2581815	0.80[ASN][1000 genomes]
rs2581816	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581819	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581827	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2710313	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2710314	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2710326	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2710339	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2710346	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515041	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6799185	0.80[EUR][1000 genomes]
rs6801235	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311485	0.81[ASN][1000 genomes]
rs9823697	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9865094	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv3823	chr3:53003659-53051063	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2756989	chr3:53006055-53039455	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2759149	chr3:53006055-53039455	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2336672	ITIH4-AS1	cis	lung	GTEx
rs2336672	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2336672	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2336672	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

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	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
4	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
6	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
7	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:52975000-53008000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:52986400-53012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:52987200-53017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:52987600-53009400	Weak transcription	Placenta	Placenta
13	chr3:52987600-53014200	Weak transcription	Fetal Thymus	thymus
14	chr3:52987600-53014200	Weak transcription	Thymus	Thymus
15	chr3:52987800-53017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:52987800-53017000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:52988000-53014200	Weak transcription	Primary T cells from cord blood	blood
18	chr3:52992000-53015800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:52993800-53016800	Weak transcription	Primary B cells from cord blood	blood
20	chr3:52997200-53008200	Weak transcription	A549	lung
21	chr3:52999000-53008200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:53001400-53008000	Weak transcription	Osteobl	bone
23	chr3:53001800-53008800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:53002000-53017600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:53002400-53012000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:53002400-53013400	Weak transcription	Liver	Liver
27	chr3:53003400-53016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:53003400-53017000	Weak transcription	Dnd41	blood
29	chr3:53004000-53012200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:53004200-53014800	Weak transcription	Fetal Intestine Small	intestine
31	chr3:53006000-53008200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr3:53006200-53015600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:53006400-53008000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:53006400-53012000	Weak transcription	Fetal Heart	heart
35	chr3:53007800-53008400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:53007800-53008400	Enhancers	Hela-S3	cervix
37	chr3:53007800-53008600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:53007800-53008600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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