Variant report

Variant	rs9812878
Chromosome Location	chr3:47182787-47182788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47181313..47183259-chr3:47377303..47380190,2	K562	blood:
2	chr3:47175740..47177368-chr3:47181984..47183489,2	K562	blood:
3	chr3:47181264..47183040-chr3:47204354..47206235,2	K562	blood:

Variant related genes	Relation type
ENSG00000227398	Chromatin interaction
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10433549	0.87[ASN][1000 genomes]
rs11130114	0.81[EUR][1000 genomes]
rs11130115	0.81[EUR][1000 genomes]
rs11707736	0.94[ASN][1000 genomes]
rs11708451	0.81[EUR][1000 genomes]
rs11709660	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11712716	0.81[EUR][1000 genomes]
rs11713693	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714373	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11715121	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11716539	0.81[EUR][1000 genomes]
rs11718795	0.80[EUR][1000 genomes]
rs11719306	0.81[EUR][1000 genomes]
rs11719738	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11720139	0.88[ASN][1000 genomes]
rs11917361	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11920354	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11923706	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925560	0.82[ASN][1000 genomes]
rs12493425	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629262	0.81[EUR][1000 genomes]
rs12631730	0.84[ASN][1000 genomes]
rs12715421	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13062022	0.81[EUR][1000 genomes]
rs13084117	0.81[EUR][1000 genomes]
rs1466740	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1466741	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17784127	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1811652	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088135	0.80[ASN][1000 genomes]
rs2278963	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2305635	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4018905	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682852	0.81[EUR][1000 genomes]
rs4683320	0.81[EUR][1000 genomes]
rs4683322	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs55724164	0.87[ASN][1000 genomes]
rs55927279	0.91[ASN][1000 genomes]
rs56217494	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56249396	0.92[ASN][1000 genomes]
rs56250009	0.80[ASN][1000 genomes]
rs57756484	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58956475	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59299766	0.82[ASN][1000 genomes]
rs62246398	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs62246451	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246455	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62248905	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6414435	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6414436	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442055	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6442059	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442060	0.88[ASN][1000 genomes]
rs6766230	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767218	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6767907	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768722	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6772670	0.81[EUR][1000 genomes]
rs6773521	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6777145	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6781941	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791062	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069104	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7373821	0.85[ASN][1000 genomes]
rs7433300	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs749511	0.88[ASN][1000 genomes]
rs749512	0.88[ASN][1000 genomes]
rs7610620	0.94[ASN][1000 genomes]
rs7620997	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621911	0.82[AFR][1000 genomes]
rs7623888	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7632501	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7633435	0.94[ASN][1000 genomes]
rs9311403	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818382	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9821119	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837343	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843075	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844122	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9845728	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9854790	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9858443	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9875235	0.87[AFR][1000 genomes];0.96[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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9812878	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs9812878	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47155400-47183800	Weak transcription	Esophagus	oesophagus
2	chr3:47165800-47187000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:47165800-47191000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:47165800-47197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:47166000-47182800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:47166000-47183000	Weak transcription	Fetal Kidney	kidney
7	chr3:47166000-47200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:47166000-47201200	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:47166000-47204600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:47166200-47197200	Weak transcription	Aorta	Aorta
11	chr3:47166200-47200600	Weak transcription	Hela-S3	cervix
12	chr3:47166400-47194200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:47166600-47182800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:47166600-47204200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:47167400-47202400	Weak transcription	HSMM	muscle
16	chr3:47167800-47187600	Weak transcription	Fetal Stomach	stomach
17	chr3:47167800-47195400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:47170200-47182800	Weak transcription	Dnd41	blood
19	chr3:47170200-47183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:47172600-47183200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:47173600-47191000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:47175800-47200400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:47176400-47190800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:47176600-47184600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:47177400-47182800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:47177400-47182800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:47177800-47182800	Weak transcription	K562	blood
28	chr3:47177800-47194200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:47178000-47182800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:47178000-47182800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:47178000-47182800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:47178000-47183400	Weak transcription	Brain Substantia Nigra	brain
33	chr3:47178000-47190800	Weak transcription	Right Ventricle	heart
34	chr3:47178000-47194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:47178200-47182800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:47178200-47183400	Weak transcription	NHEK	skin
37	chr3:47178400-47183600	Weak transcription	Left Ventricle	heart
38	chr3:47178600-47183600	Weak transcription	Spleen	Spleen
39	chr3:47178600-47187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:47178600-47188200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:47178600-47190600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:47180000-47184000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:47180000-47188400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:47180400-47183800	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr3:47180400-47185000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:47180400-47185000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:47180400-47186200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:47180600-47185800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:47180800-47183000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:47180800-47183000	Enhancers	NHDF-Ad	bronchial

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