Variant report

Variant	rs6773040
Chromosome Location	chr3:52935428-52935429
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52933827..52935933-chr3:53105479..53107077,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITIH3-4	chr3:52935338-52935791	NONHSAT089973

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11130332	0.86[EUR][1000 genomes]
rs1134546	0.98[EUR][1000 genomes]
rs11707576	0.84[EUR][1000 genomes]
rs11708223	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13082061	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2336162	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336666	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2336669	0.83[EUR][1000 genomes]
rs2336671	0.82[EUR][1000 genomes]
rs2564947	0.81[EUR][1000 genomes]
rs2581797	0.86[EUR][1000 genomes]
rs2581801	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2581802	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2581805	0.85[EUR][1000 genomes]
rs2581810	0.90[EUR][1000 genomes]
rs2581815	0.86[EUR][1000 genomes]
rs2581820	0.83[EUR][1000 genomes]
rs2581823	0.82[EUR][1000 genomes]
rs2710342	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2710345	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2878762	0.83[AMR][1000 genomes]
rs35380116	0.83[EUR][1000 genomes]
rs4302374	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4519686	0.84[EUR][1000 genomes]
rs4687559	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687560	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687692	0.81[EUR][1000 genomes]
rs6445547	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6445550	0.84[EUR][1000 genomes]
rs6768844	0.84[EUR][1000 genomes]
rs6770957	0.84[EUR][1000 genomes]
rs6771610	0.83[EUR][1000 genomes]
rs6792578	0.84[EUR][1000 genomes]
rs6797399	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7621939	0.85[EUR][1000 genomes]
rs7648514	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7652131	0.84[EUR][1000 genomes]
rs9311485	0.85[EUR][1000 genomes]
rs9682464	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9812543	0.84[EUR][1000 genomes]
rs9831409	0.86[EUR][1000 genomes]
rs9836178	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839035	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9842974	0.84[EUR][1000 genomes]
rs9844736	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9846976	0.84[EUR][1000 genomes]
rs9847024	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865094	0.84[EUR][1000 genomes]
rs9876403	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9985365	0.81[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6773040	ITIH4-AS1	cis	lung	GTEx
rs6773040	MUSTN1	cis	Artery Aorta	GTEx
rs6773040	ITIH4-AS1	cis	Artery Tibial	GTEx
rs6773040	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931600-52945000	Weak transcription	Gastric	stomach
2	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
3	chr3:52932000-52936200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:52932000-52937000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:52932000-52938200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:52932000-52938600	Weak transcription	Left Ventricle	heart
7	chr3:52932000-52938800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:52932000-52939000	Weak transcription	Aorta	Aorta
9	chr3:52932000-52939000	Weak transcription	Psoas Muscle	Psoas
10	chr3:52932000-52940000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:52932000-52941000	Weak transcription	Lung	lung
12	chr3:52932000-52943600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:52932000-52943800	Weak transcription	Pancreas	Pancrea
14	chr3:52932000-52946400	Weak transcription	Esophagus	oesophagus
15	chr3:52932000-52953400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:52932000-52954000	Weak transcription	Small Intestine	intestine
17	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:52932200-52935800	Weak transcription	Fetal Brain Female	brain
21	chr3:52932200-52936000	Weak transcription	Primary T cells from cord blood	blood
22	chr3:52932200-52936200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:52932200-52936200	Weak transcription	Liver	Liver
24	chr3:52932200-52936200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:52932200-52936800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:52932200-52937200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:52932200-52937400	Weak transcription	Primary B cells from cord blood	blood
28	chr3:52932200-52937600	Weak transcription	HepG2	liver
29	chr3:52932200-52937600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:52932200-52937800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:52932200-52937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:52932200-52937800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:52932200-52937800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:52932200-52937800	Weak transcription	Placenta	Placenta
35	chr3:52932200-52938000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:52932200-52938000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:52932200-52938000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:52932200-52938000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:52932200-52938000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:52932200-52938000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:52932200-52938200	Weak transcription	Fetal Intestine Small	intestine
42	chr3:52932200-52938800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:52932200-52939000	Weak transcription	GM12878-XiMat	blood
44	chr3:52932200-52939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:52932200-52940000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:52932200-52940200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:52932200-52940200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:52932200-52940800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:52932200-52941000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:52932200-52946000	Weak transcription	Colon Smooth Muscle	Colon

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