Variant report

Variant	rs6801235
Chromosome Location	chr3:53009595-53009596
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: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2245424	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2246556	0.86[ASN][1000 genomes]
rs2257216	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2336670	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2336672	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2439434	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465101	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2564930	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2581803	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581816	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581819	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2581827	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710313	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710314	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710326	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2710339	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2710346	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4515041	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6799185	0.80[EUR][1000 genomes]
rs9823697	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828491	0.84[ASN][1000 genomes]
rs9846976	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv998445	chr3:53008146-53023199	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1001449	chr3:53009379-53039104	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking 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
rs6801235	ITIH4-AS1	cis	Artery Aorta	GTEx
rs6801235	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs6801235	ITIH4-AS1	cis	Artery Tibial	GTEx
rs6801235	ITIH4-AS1	cis	lung	GTEx

Chromatin state (count:33 , 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	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:52986400-53012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:52987200-53017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:52987600-53014200	Weak transcription	Fetal Thymus	thymus
10	chr3:52987600-53014200	Weak transcription	Thymus	Thymus
11	chr3:52987800-53017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:52987800-53017000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52988000-53014200	Weak transcription	Primary T cells from cord blood	blood
14	chr3:52992000-53015800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:52993800-53016800	Weak transcription	Primary B cells from cord blood	blood
16	chr3:53002000-53017600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:53002400-53012000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:53002400-53013400	Weak transcription	Liver	Liver
19	chr3:53003400-53016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:53003400-53017000	Weak transcription	Dnd41	blood
21	chr3:53004000-53012200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:53004200-53014800	Weak transcription	Fetal Intestine Small	intestine
23	chr3:53006200-53015600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:53006400-53012000	Weak transcription	Fetal Heart	heart
25	chr3:53008200-53015800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:53008400-53031000	Weak transcription	Hela-S3	cervix
27	chr3:53008600-53016000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:53008800-53009800	Enhancers	A549	lung
29	chr3:53009000-53009800	Enhancers	HepG2	liver
30	chr3:53009400-53009600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:53009400-53009800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:53009400-53010000	Enhancers	Placenta	Placenta
33	chr3:53009400-53016000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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