Variant report

Variant	rs1873076
Chromosome Location	chr3:160098537-160098538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160093951..160095466-chr3:160097578..160100383,2	K562	blood:
2	chr3:160093908..160095466-chr3:160097578..160100691,3	K562	blood:
3	chr3:160089762..160091914-chr3:160096661..160098564,2	K562	blood:

Variant related genes	Relation type
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1047210	0.81[JPT][hapmap]
rs10923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10936201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11706810	0.81[JPT][hapmap]
rs11708118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11709232	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11716413	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11720689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12152435	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12630564	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12630770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12630956	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12632030	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12638633	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12639488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs16831207	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236494	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17826137	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17826173	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17826221	0.81[JPT][hapmap]
rs17826257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2095529	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2099496	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2275151	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732706	1.00[ASW][hapmap];0.84[YRI][hapmap]
rs3773369	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679886	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679892	0.82[EUR][1000 genomes]
rs4680581	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680586	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56952700	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60395700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441311	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6798183	0.81[JPT][hapmap]
rs6809153	0.81[JPT][hapmap]
rs73875254	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73875259	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73875285	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73875290	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7620828	0.81[JPT][hapmap]
rs7627555	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1873076	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
3	chr3:160066400-160099200	Weak transcription	NHEK	skin
4	chr3:160069000-160115200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:160071400-160102000	Weak transcription	Small Intestine	intestine
6	chr3:160071600-160099400	Weak transcription	Placenta	Placenta
7	chr3:160073400-160099200	Weak transcription	HSMMtube	muscle
8	chr3:160073800-160108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:160074800-160101400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:160076200-160116200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:160081200-160102200	Weak transcription	HUVEC	blood vessel
12	chr3:160081800-160100000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:160083400-160113000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:160083800-160108200	Weak transcription	GM12878-XiMat	blood
15	chr3:160083800-160116000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:160084000-160104000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:160088200-160099800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:160088800-160101400	Weak transcription	Hela-S3	cervix
19	chr3:160088800-160108600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:160088800-160108600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:160088800-160116200	Weak transcription	Primary B cells from cord blood	blood
22	chr3:160088800-160116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:160089000-160104000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:160091600-160105800	Weak transcription	Ovary	ovary
25	chr3:160092000-160113200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:160092200-160100400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:160092200-160103200	Weak transcription	K562	blood
28	chr3:160092200-160116000	Weak transcription	Fetal Stomach	stomach
29	chr3:160092200-160116200	Weak transcription	Fetal Intestine Small	intestine
30	chr3:160092200-160116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:160093000-160102800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:160093000-160113000	Weak transcription	NHLF	lung
33	chr3:160093200-160099400	Weak transcription	Liver	Liver
34	chr3:160093200-160113200	Weak transcription	Brain Germinal Matrix	brain
35	chr3:160093400-160100800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:160093600-160116000	Weak transcription	Fetal Kidney	kidney
37	chr3:160094000-160100000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:160094400-160100200	Weak transcription	Adipose Nuclei	Adipose
39	chr3:160094600-160099400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:160094600-160116000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:160094800-160100000	Weak transcription	Esophagus	oesophagus
42	chr3:160094800-160100400	Weak transcription	Brain Anterior Caudate	brain
43	chr3:160094800-160101200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:160094800-160104800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:160094800-160113000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:160094800-160113200	Weak transcription	HSMM	muscle
47	chr3:160094800-160115800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:160094800-160116000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:160094800-160116000	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:160094800-160116600	Weak transcription	Left Ventricle	heart

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