Variant report

Variant	rs11922975
Chromosome Location	chr3:52936763-52936764
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	chr3:52935990..52938094-chr3:53078849..53080891,2	K562	blood:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10865977	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130331	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11918800	0.92[CEU][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs11922961	0.92[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs12487379	0.85[EUR][1000 genomes]
rs12492391	0.96[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12629687	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638968	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13072537	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13083728	0.82[JPT][hapmap]
rs1573815	0.82[JPT][hapmap]
rs2071042	0.92[CEU][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs2239547	0.82[JPT][hapmap]
rs2240915	0.91[CEU][hapmap]
rs2256332	0.82[CHD][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs2257216	0.88[ASW][hapmap];0.80[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap]
rs2276815	0.82[JPT][hapmap]
rs2276817	0.82[JPT][hapmap]
rs2276825	0.82[JPT][hapmap]
rs2336664	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2336667	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2336668	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2336670	0.81[CEU][hapmap];0.93[YRI][hapmap]
rs2535633	0.92[CEU][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs2581815	0.80[GIH][hapmap]
rs2710314	0.80[CEU][hapmap]
rs3733047	0.82[JPT][hapmap]
rs3821873	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4302374	0.86[JPT][hapmap]
rs4350911	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4687554	0.82[JPT][hapmap]
rs4687562	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4687657	0.82[JPT][hapmap]
rs4687658	0.82[JPT][hapmap]
rs4687672	0.82[JPT][hapmap]
rs4687679	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687680	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4687682	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687683	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687684	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687689	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56383738	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253583	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445538	0.82[JPT][hapmap]
rs6445539	0.82[JPT][hapmap]
rs6445541	0.92[CEU][hapmap]
rs6445547	0.86[JPT][hapmap]
rs6764322	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6769789	0.92[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs6773650	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6795646	0.96[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6799185	0.80[CEU][hapmap];0.82[GIH][hapmap]
rs6803519	0.82[JPT][hapmap]
rs7612624	0.81[AMR][1000 genomes]
rs7620690	0.80[EUR][1000 genomes]
rs7626551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630552	0.80[EUR][1000 genomes]
rs9682464	0.82[JPT][hapmap]
rs9810807	0.95[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9823697	0.88[ASW][hapmap];0.80[CEU][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap]
rs9825230	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9836499	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9844736	0.95[JPT][hapmap]
rs9850563	0.96[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9860296	0.96[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9865248	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9866243	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9871175	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876403	0.86[JPT][hapmap]
rs9880619	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9880978	0.96[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9985365	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11922975	ITIH4	cis	cerebellum	SCAN
rs11922975	TEX264	cis	parietal	SCAN
rs11922975	ITIH4-AS1	cis	lung	GTEx
rs11922975	ITIH4-AS1	cis	Artery Tibial	GTEx
rs11922975	SFMBT1	cis	cerebellum	SCAN
rs11922975	GNL3	cis	cerebellum	SCAN
rs11922975	ITIH4	cis	lymphoblastoid	seeQTL
rs11922975	GNL3	cis	parietal	SCAN
rs11922975	ITIH4-AS1	cis	Artery Aorta	GTEx
rs11922975	SEMA3G	cis	parietal	SCAN
rs11922975	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:52932000-52937000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:52932000-52938200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:52932000-52938600	Weak transcription	Left Ventricle	heart
6	chr3:52932000-52938800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:52932000-52939000	Weak transcription	Aorta	Aorta
8	chr3:52932000-52939000	Weak transcription	Psoas Muscle	Psoas
9	chr3:52932000-52940000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:52932000-52941000	Weak transcription	Lung	lung
11	chr3:52932000-52943600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:52932000-52943800	Weak transcription	Pancreas	Pancrea
13	chr3:52932000-52946400	Weak transcription	Esophagus	oesophagus
14	chr3:52932000-52953400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:52932000-52954000	Weak transcription	Small Intestine	intestine
16	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:52932200-52936800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:52932200-52937200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:52932200-52937400	Weak transcription	Primary B cells from cord blood	blood
22	chr3:52932200-52937600	Weak transcription	HepG2	liver
23	chr3:52932200-52937600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr3:52932200-52937800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:52932200-52937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:52932200-52937800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:52932200-52937800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:52932200-52937800	Weak transcription	Placenta	Placenta
29	chr3:52932200-52938000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:52932200-52938000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:52932200-52938000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:52932200-52938000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:52932200-52938000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:52932200-52938000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:52932200-52938200	Weak transcription	Fetal Intestine Small	intestine
36	chr3:52932200-52938800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:52932200-52939000	Weak transcription	GM12878-XiMat	blood
38	chr3:52932200-52939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:52932200-52940000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:52932200-52940200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:52932200-52940200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:52932200-52940800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:52932200-52941000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:52932200-52946000	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:52932200-52948600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:52932200-52948800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:52932200-52951400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:52932200-52952800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:52932200-52953600	Weak transcription	Right Ventricle	heart
50	chr3:52932200-52953800	Weak transcription	Ovary	ovary

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