Variant report

Variant	rs9852082
Chromosome Location	chr3:46972377-46972378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

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	chr3:46972031..46974044-chr3:46975427..46977474,2	K562	blood:
4	chr3:46971685..46974752-chr3:47019618..47022746,3	MCF-7	breast:
5	chr3:46966739..46968792-chr3:46972024..46974475,2	K562	blood:
6	chr3:46971793..46974784-chr3:46975168..46977943,4	MCF-7	breast:
7	chr3:46733445..46736212-chr3:46971481..46974071,3	MCF-7	breast:
8	chr3:46962526..46964084-chr3:46970657..46972462,2	K562	blood:
9	chr3:46970325..46973197-chr3:47005456..47008384,2	MCF-7	breast:
10	chr3:46970409..46973424-chr3:46974292..46976174,3	K562	blood:
11	chr3:46971047..46973675-chr3:47000415..47002568,2	MCF-7	breast:
12	chr3:46964095..46966597-chr3:46971583..46973644,2	K562	blood:
13	chr3:46965569..46968989-chr3:46970425..46974513,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000178038	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1001284	0.92[ASN][1000 genomes]
rs10461018	0.86[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs1079276	0.81[JPT][hapmap]
rs10865943	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130110	0.86[JPT][hapmap]
rs11130111	0.82[JPT][hapmap]
rs1138518	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11705936	0.98[ASN][1000 genomes]
rs11719795	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11720139	0.85[YRI][hapmap]
rs12491473	0.81[AFR][1000 genomes]
rs13061071	0.81[JPT][hapmap]
rs1463393	0.81[AFR][1000 genomes]
rs1466275	0.90[ASN][1000 genomes]
rs2061197	0.86[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2168443	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2242116	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2278963	0.86[YRI][hapmap]
rs2290545	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2290546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305634	0.81[JPT][hapmap]
rs2305638	0.81[JPT][hapmap]
rs4078466	0.81[JPT][hapmap]
rs4082155	0.81[JPT][hapmap]
rs4539969	0.90[ASN][1000 genomes]
rs4587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682837	0.83[JPT][hapmap]
rs4682844	0.86[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs4682845	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683294	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs4683296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683298	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683299	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683300	0.91[ASN][1000 genomes]
rs4683301	0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4683322	0.86[YRI][hapmap]
rs62248439	0.81[AFR][1000 genomes]
rs6442038	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442039	0.90[ASN][1000 genomes]
rs6442040	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6767907	0.86[YRI][hapmap]
rs6780601	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724448	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs724449	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs724450	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7433300	0.86[YRI][hapmap]
rs749512	0.95[YRI][hapmap]
rs7623898	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628747	0.86[JPT][hapmap]
rs7635480	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646906	0.93[ASN][1000 genomes]
rs9311403	0.82[YRI][hapmap]
rs9855938	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9852082	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs9852082	SETD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46962600-46972400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:46962800-46972400	Weak transcription	Fetal Kidney	kidney
3	chr3:46964600-46975600	Weak transcription	Fetal Brain Male	brain
4	chr3:46964800-46972800	Enhancers	Fetal Heart	heart
5	chr3:46967000-46972400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:46967400-46974600	Enhancers	HSMMtube	muscle
7	chr3:46967400-46975800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:46967400-46976000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:46967400-46976400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:46967400-46984400	Genic enhancers	Fetal Intestine Small	intestine
11	chr3:46967800-46976400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:46968000-46978800	Enhancers	Stomach Mucosa	stomach
13	chr3:46968400-46975800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:46968400-46976600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:46968400-46977600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:46968600-46975400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr3:46969200-46972800	Weak transcription	NHEK	skin
18	chr3:46969200-46976600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:46969200-46976600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr3:46969400-46972400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:46969400-46973000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:46969400-46973800	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:46969400-46974400	Enhancers	Colonic Mucosa	Colon
24	chr3:46969400-46978400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:46969600-46977400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr3:46969800-46972600	ZNF genes & repeats	GM12878-XiMat	blood
27	chr3:46970000-46972800	Weak transcription	Brain Germinal Matrix	brain
28	chr3:46970200-46973000	Enhancers	Brain Anterior Caudate	brain
29	chr3:46970200-46973400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:46970200-46973400	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:46970200-46976800	Enhancers	Brain Hippocampus Middle	brain
32	chr3:46970200-46978600	Enhancers	Right Ventricle	heart
33	chr3:46970400-46972400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:46970400-46973600	Weak transcription	Fetal Brain Female	brain
35	chr3:46970400-46976400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:46970400-46977600	Enhancers	Liver	Liver
37	chr3:46970400-46977800	Enhancers	Pancreas	Pancrea
38	chr3:46970600-46973200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr3:46970600-46975000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:46970600-46975200	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:46970600-46977600	Enhancers	Brain Angular Gyrus	brain
42	chr3:46970800-46972400	Enhancers	Fetal Muscle Leg	muscle
43	chr3:46970800-46972600	Enhancers	Colon Smooth Muscle	Colon
44	chr3:46970800-46974200	Enhancers	Aorta	Aorta
45	chr3:46970800-46975800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr3:46970800-46976200	Enhancers	Spleen	Spleen
47	chr3:46970800-46977400	Enhancers	Placenta	Placenta
48	chr3:46970800-46977600	Enhancers	Left Ventricle	heart
49	chr3:46970800-46977600	Enhancers	Lung	lung
50	chr3:46970800-46977800	Enhancers	NHDF-Ad	bronchial

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