Variant report

Variant	rs1877362
Chromosome Location	chr3:112331590-112331591
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	chr3:112317258..112319990-chr3:112330673..112332621,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10934177	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385527	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386896	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1388442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488260	1.00[ASN][1000 genomes]
rs1488262	1.00[ASN][1000 genomes]
rs1491629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532198	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814053	1.00[ASN][1000 genomes]
rs1817694	1.00[ASN][1000 genomes]
rs1844864	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906519	1.00[ASN][1000 genomes]
rs2029317	1.00[ASN][1000 genomes]
rs2399431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464612	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638025	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638030	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638033	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638036	1.00[ASN][1000 genomes]
rs2638038	1.00[CHB][hapmap]
rs2638041	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638043	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2638044	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705506	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705514	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705524	1.00[ASN][1000 genomes]
rs2705551	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933139	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933140	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969894	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109033	0.86[ASN][1000 genomes]
rs62264580	0.83[ASN][1000 genomes]
rs6793232	1.00[ASN][1000 genomes]
rs7612851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7618978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901829	1.00[ASN][1000 genomes]
rs971832	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986883	1.00[EUR][1000 genomes];1.00[ASN][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	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1877362	CD3D	trans	lymphoblastoid	seeQTL
rs1877362	DSC3	trans	lymphoblastoid	seeQTL
rs1877362	HBD	trans	lymphoblastoid	seeQTL
rs1877362	SYPL2	trans	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
4	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
5	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
7	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:112316400-112333600	Weak transcription	A549	lung
9	chr3:112316600-112337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:112318000-112341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:112322200-112337200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:112323400-112332400	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr3:112323800-112334600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:112324600-112331800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:112326000-112333400	Weak transcription	Ovary	ovary
16	chr3:112327200-112331600	Weak transcription	Fetal Lung	lung
17	chr3:112327800-112340600	Weak transcription	Fetal Kidney	kidney
18	chr3:112328200-112332200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:112328400-112332600	Genic enhancers	Osteobl	bone
20	chr3:112328600-112332600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:112329000-112331600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:112329000-112334400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:112329200-112333400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:112329400-112333400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:112329400-112333400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:112329400-112334200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:112329600-112341800	Strong transcription	HSMM	muscle
28	chr3:112330000-112332000	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:112330000-112335000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr3:112330000-112336600	Strong transcription	NHDF-Ad	bronchial
31	chr3:112330200-112338400	Strong transcription	HSMMtube	muscle
32	chr3:112330400-112331600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:112330400-112331600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:112330400-112331800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:112330400-112335000	Strong transcription	NH-A	brain
36	chr3:112330400-112346800	Strong transcription	NHLF	lung
37	chr3:112330600-112331600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:112330600-112331600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:112330600-112331600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:112330600-112333600	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:112331000-112331600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:112331000-112331800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
43	chr3:112331200-112331600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:112331200-112331600	Enhancers	HUVEC	blood vessel
45	chr3:112331200-112334000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:112331200-112334400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:112331200-112334800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:112331200-112335400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:112331200-112351600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:112331400-112331600	Enhancers	Adipose Nuclei	Adipose

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