Variant report

Variant	rs28615303
Chromosome Location	chr3:112022750-112022751
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr3:112021224-112022933	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOSL1	chr3:112022580-112023038	H1-hESC	embryonic stem cell:	n/a	n/a
3	TBP	chr3:112021868-112022946	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3A	chr3:112021596-112022928	H1-hESC	embryonic stem cell:	n/a	n/a
5	MTA3	chr3:112022028-112022895	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:112022745-112022830	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOSL1	chr3:112022657-112022960	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:112022647-112022879	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:112022720-112022870	HCPEpiC	choroid plexus:	n/a	n/a
10	SP1	chr3:112021863-112023047	H1-hESC	embryonic stem cell:	n/a	chr3:112022141-112022152
11	POLR2A	chr3:112022135-112023055	GM12892	blood:	n/a	n/a
12	ZNF143	chr3:112022689-112022900	Hela-S3	cervix:	n/a	n/a
13	TAF1	chr3:112022669-112022943	GM12878	blood:	n/a	n/a
14	CHD2	chr3:112021818-112022916	H1-hESC	embryonic stem cell:	n/a	n/a
15	YY1	chr3:112022689-112023199	GM12891	blood:	n/a	n/a
16	ZNF143	chr3:112022480-112022965	GM12878	blood:	n/a	n/a
17	SPI1	chr3:112022697-112022995	GM12891	blood:	n/a	n/a
18	ZNF143	chr3:112021133-112023008	H1-hESC	embryonic stem cell:	n/a	n/a
19	STAT1	chr3:112022540-112022773	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000239482	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10804498	1.00[ASN][1000 genomes]
rs10934163	1.00[ASN][1000 genomes]
rs10934164	1.00[ASN][1000 genomes]
rs10934165	1.00[ASN][1000 genomes]
rs11709101	1.00[ASN][1000 genomes]
rs11717777	1.00[ASN][1000 genomes]
rs11720514	1.00[ASN][1000 genomes]
rs11923402	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497979	1.00[ASN][1000 genomes]
rs13084103	1.00[ASN][1000 genomes]
rs1317295	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317658	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316383	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492479	1.00[ASN][1000 genomes]
rs17513880	1.00[ASN][1000 genomes]
rs2399419	1.00[ASN][1000 genomes]
rs2633546	1.00[ASN][1000 genomes]
rs2683891	1.00[ASN][1000 genomes]
rs2683892	1.00[ASN][1000 genomes]
rs4507229	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622877	1.00[ASN][1000 genomes]
rs4682393	1.00[ASN][1000 genomes]
rs4682400	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56008438	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56294743	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56364691	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	1.00[ASN][1000 genomes]
rs60949597	1.00[ASN][1000 genomes]
rs62262366	1.00[ASN][1000 genomes]
rs62262408	1.00[ASN][1000 genomes]
rs62262411	1.00[ASN][1000 genomes]
rs62264125	1.00[ASN][1000 genomes]
rs62264128	1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62278765	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278768	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278770	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278771	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278843	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438072	1.00[ASN][1000 genomes]
rs6766013	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6795820	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223638	1.00[ASN][1000 genomes]
rs7609904	1.00[ASN][1000 genomes]
rs7612748	1.00[ASN][1000 genomes]
rs7621431	1.00[ASN][1000 genomes]
rs7631673	1.00[ASN][1000 genomes]
rs7636107	1.00[ASN][1000 genomes]
rs7650962	1.00[ASN][1000 genomes]
rs7651121	1.00[ASN][1000 genomes]
rs9810421	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816969	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818407	1.00[ASN][1000 genomes]
rs9823824	1.00[ASN][1000 genomes]
rs9829698	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837134	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9843666	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9851760	1.00[ASN][1000 genomes]
rs9853669	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855755	1.00[ASN][1000 genomes]
rs9871088	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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv967052	chr3:112020436-112027937	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28615303	C6orf106	trans	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112021000-112023000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr3:112021200-112023400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr3:112021400-112023000	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:112021400-112023200	Active TSS	Colon Smooth Muscle	Colon
5	chr3:112021400-112023200	Flanking Active TSS	Fetal Thymus	thymus
6	chr3:112021400-112023400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr3:112021400-112025200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:112021600-112023000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:112021600-112023000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:112021600-112023000	Active TSS	Right Atrium	heart
11	chr3:112021600-112023200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:112021600-112023400	Active TSS	Fetal Brain Female	brain
13	chr3:112021600-112023400	Active TSS	Rectal Smooth Muscle	rectum
14	chr3:112021600-112023600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:112021800-112022800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:112021800-112022800	Active TSS	Hela-S3	cervix
17	chr3:112021800-112023000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:112021800-112023000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:112021800-112023000	Active TSS	Aorta	Aorta
20	chr3:112021800-112023000	Active TSS	Placenta	Placenta
21	chr3:112021800-112023200	Active TSS	Colonic Mucosa	Colon
22	chr3:112021800-112023400	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr3:112021800-112023400	Active TSS	Left Ventricle	heart
24	chr3:112021800-112023400	Flanking Active TSS	HUVEC	blood vessel
25	chr3:112021800-112023600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:112021800-112023600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr3:112021800-112023600	Enhancers	Lung	lung
28	chr3:112021800-112023600	Active TSS	Psoas Muscle	Psoas
29	chr3:112022000-112022800	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr3:112022000-112022800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr3:112022000-112022800	Active TSS	Fetal Stomach	stomach
32	chr3:112022000-112023000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:112022000-112023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:112022000-112023000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:112022000-112023000	Active TSS	Fetal Lung	lung
36	chr3:112022000-112023200	Enhancers	Liver	Liver
37	chr3:112022000-112023200	Active TSS	Brain Hippocampus Middle	brain
38	chr3:112022000-112023200	Active TSS	Fetal Intestine Large	intestine
39	chr3:112022000-112023200	Active TSS	Fetal Muscle Trunk	muscle
40	chr3:112022000-112023400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr3:112022000-112023400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr3:112022000-112023400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:112022000-112023400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:112022000-112023400	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr3:112022000-112023400	Active TSS	Fetal Kidney	kidney
46	chr3:112022000-112023400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:112022000-112023600	Active TSS	Fetal Intestine Small	intestine
48	chr3:112022200-112022800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr3:112022200-112022800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr3:112022200-112022800	Flanking Active TSS	HMEC	breast

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