Variant report

Variant	rs10865943
Chromosome Location	chr3:46969970-46969971
allele	C/T
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	POLR2A	chr3:46966735-46970133	GM12878	blood:	n/a	n/a
2	ATF2	chr3:46969828-46970287	GM12878	blood:	n/a	n/a
3	MAX	chr3:46969886-46970243	GM12878	blood:	n/a	n/a
4	PAX5	chr3:46969782-46970189	GM12878	blood:	n/a	n/a
5	E2F4	chr3:46969876-46970175	GM12878	blood:	n/a	n/a
6	CBX3	chr3:46969868-46970245	K562	blood:	n/a	n/a
7	RCOR1	chr3:46969771-46970176	GM12878	blood:	n/a	n/a
8	ZNF143	chr3:46969932-46970230	K562	blood:	n/a	n/a
9	RUNX3	chr3:46969662-46970215	GM12878	blood:	n/a	n/a
10	MTA3	chr3:46966876-46970269	GM12878	blood:	n/a	n/a
11	KAP1	chr3:46969767-46970271	K562	blood:	n/a	n/a
12	MAZ	chr3:46969891-46970198	GM12878	blood:	n/a	n/a
13	BCLAF1	chr3:46969704-46970363	GM12878	blood:	n/a	n/a
14	NFIC	chr3:46968093-46970282	GM12878	blood:	n/a	n/a
15	BCLAF1	chr3:46969729-46970253	GM12878	blood:	n/a	n/a
16	ATF2	chr3:46969695-46970252	GM12878	blood:	n/a	n/a
17	FOXM1	chr3:46969715-46970257	GM12878	blood:	n/a	n/a
18	STAT5A	chr3:46969846-46970326	GM12878	blood:	n/a	n/a
19	TBP	chr3:46969899-46970264	GM12878	blood:	n/a	n/a
20	ZNF384	chr3:46969879-46970246	K562	blood:	n/a	n/a
21	POLR2A	chr3:46956505-46971093	K562	blood:	n/a	n/a
22	STAT5A	chr3:46967744-46970468	GM12878	blood:	n/a	chr3:46967978-46967986 chr3:46968254-46968266 chr3:46968830-46968841 chr3:46968696-46968708 chr3:46968403-46968410 chr3:46968086-46968109 chr3:46968321-46968329
23	SMC3	chr3:46969889-46970220	GM12878	blood:	n/a	n/a
24	MEF2A	chr3:46969772-46970159	GM12878	blood:	n/a	n/a
25	STAT1	chr3:46969885-46970079	GM12878	blood:	n/a	n/a
26	EBF1	chr3:46969758-46970259	GM12878	blood:	n/a	chr3:46970012-46970023
27	IKZF1	chr3:46969734-46970156	GM12878	blood:	n/a	n/a
28	EP300	chr3:46969855-46970064	GM12878	blood:	n/a	n/a
29	EBF1	chr3:46969766-46970132	GM12878	blood:	n/a	chr3:46970012-46970023
30	ZNF143	chr3:46969894-46970258	GM12878	blood:	n/a	n/a
31	USF2	chr3:46969948-46970012	K562	blood:	n/a	n/a
32	POLR2A	chr3:46966882-46970456	GM12891	blood:	n/a	n/a
33	TBL1XR1	chr3:46969741-46970197	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:46966435-46970329	GM18505	blood:	n/a	n/a
35	BHLHE40	chr3:46969837-46970265	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:46966707-46970065	GM12878	blood:	n/a	n/a
37	CHD2	chr3:46969853-46970159	GM12878	blood:	n/a	n/a
38	PAX5	chr3:46969805-46970161	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:46969621-46970309	HL-60	blood:	n/a	n/a
40	EBF1	chr3:46969770-46970171	GM12878	blood:	n/a	chr3:46970012-46970023
41	STAT3	chr3:46969794-46970290	GM12878	blood:	n/a	n/a
42	WRNIP1	chr3:46969789-46970037	GM12878	blood:	n/a	n/a
43	PML	chr3:46967258-46970154	GM12878	blood:	n/a	chr3:46967474-46967482
44	YY1	chr3:46969755-46970161	GM12878	blood:	n/a	n/a
45	EP300	chr3:46969818-46970166	GM12878	blood:	n/a	n/a
46	EP300	chr3:46969785-46970197	GM12878	blood:	n/a	n/a
47	MXI1	chr3:46969762-46970151	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:46969853-46970064	A549	lung:	n/a	n/a
49	ZNF384	chr3:46969728-46970275	GM12878	blood:	n/a	n/a
50	RUNX3	chr3:46969699-46970268	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46968433..46974874-chr3:46985986..46991697,10	MCF-7	breast:
2	chr3:46967009..46980239-chr3:47015804..47024437,23	MCF-7	breast:
3	chr3:46964830..46966605-chr3:46968655..46970497,2	K562	blood:
4	chr3:46968346..46971125-chr3:47016848..47020508,3	K562	blood:
5	chr3:46968594..46970505-chr3:47016848..47019482,2	K562	blood:
6	chr3:46969295..46972082-chr3:46977350..46978888,2	K562	blood:

Variant related genes	Relation type
CCDC12	TF binding region
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1001284	0.94[ASN][1000 genomes]
rs1138518	0.92[ASN][1000 genomes]
rs11705936	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719795	0.95[ASN][1000 genomes]
rs1466275	0.92[ASN][1000 genomes]
rs2242116	0.92[ASN][1000 genomes]
rs2290545	0.89[ASN][1000 genomes]
rs2290546	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4539969	0.89[ASN][1000 genomes]
rs4587	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682845	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683296	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683297	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683298	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683299	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683300	0.92[ASN][1000 genomes]
rs4683301	0.88[ASN][1000 genomes]
rs6442038	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442039	0.89[ASN][1000 genomes]
rs6442040	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780601	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724448	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs724449	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs724450	0.92[ASN][1000 genomes]
rs7623898	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7635480	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7645278	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7646906	0.94[ASN][1000 genomes]
rs9852082	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855938	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10865943	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46958600-46970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:46959000-46971400	Strong transcription	K562	blood
3	chr3:46959600-46970600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:46959800-46971200	Strong transcription	Hela-S3	cervix
5	chr3:46960200-46971200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:46960400-46970400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:46960400-46970400	Strong transcription	Fetal Lung	lung
8	chr3:46961000-46970000	Strong transcription	Brain Germinal Matrix	brain
9	chr3:46961400-46970400	Strong transcription	Fetal Brain Female	brain
10	chr3:46961800-46971200	Strong transcription	HepG2	liver
11	chr3:46962600-46972400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:46962800-46972400	Weak transcription	Fetal Kidney	kidney
13	chr3:46964000-46970200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:46964200-46970000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:46964600-46975600	Weak transcription	Fetal Brain Male	brain
16	chr3:46964800-46972800	Enhancers	Fetal Heart	heart
17	chr3:46965000-46971200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:46965400-46970000	Genic enhancers	Esophagus	oesophagus
19	chr3:46965800-46970000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:46966400-46971400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:46966600-46970000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:46966600-46970000	Genic enhancers	Fetal Thymus	thymus
23	chr3:46967000-46970800	Weak transcription	Aorta	Aorta
24	chr3:46967000-46972400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:46967200-46970200	Enhancers	Psoas Muscle	Psoas
26	chr3:46967200-46970800	Weak transcription	HMEC	breast
27	chr3:46967200-46971200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:46967200-46971800	Weak transcription	Ovary	ovary
29	chr3:46967400-46971800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:46967400-46974600	Enhancers	HSMMtube	muscle
31	chr3:46967400-46975800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:46967400-46976000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:46967400-46976400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:46967400-46984400	Genic enhancers	Fetal Intestine Small	intestine
35	chr3:46967600-46970200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr3:46967600-46970400	Genic enhancers	Primary T cells from cord blood	blood
37	chr3:46967600-46971000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:46967600-46971000	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr3:46967800-46971200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr3:46967800-46976400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:46968000-46970000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:46968000-46972000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:46968000-46978800	Enhancers	Stomach Mucosa	stomach
44	chr3:46968200-46970000	Enhancers	Brain Substantia Nigra	brain
45	chr3:46968200-46971200	Genic enhancers	Dnd41	blood
46	chr3:46968200-46971800	Enhancers	Duodenum Mucosa	Duodenum
47	chr3:46968400-46970400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:46968400-46970800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:46968400-46971000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:46968400-46971200	Strong transcription	NHLF	lung

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