Variant report

Variant	rs3132540
Chromosome Location	chr6:31109943-31109944
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	chr6:31109805-31109968	K562	blood:	n/a	n/a
2	POLR2A	chr6:31109731-31109997	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:31109578-31110015	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31096272..31098669-chr6:31109725..31111701,2	MCF-7	breast:
2	chr6:31107129..31110169-chr6:31111741..31115408,4	K562	blood:
3	chr6:31107022..31110169-chr6:31112293..31115408,4	K562	blood:
4	chr6:31106197..31108708-chr6:31109139..31110645,2	MCF-7	breast:

Variant related genes	Relation type
PSORS1C2	TF binding region
ENSG00000204536	Chromatin interaction
ENSG00000238211	Chromatin interaction
ENSG00000204538	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2073722	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2233942	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240062	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240065	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094227	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094606	0.83[ASN][1000 genomes]
rs3094607	0.86[ASN][1000 genomes]
rs3094608	0.87[ASN][1000 genomes]
rs3094609	0.90[ASN][1000 genomes]
rs3094610	0.86[ASN][1000 genomes]
rs3095237	0.90[ASN][1000 genomes]
rs3095238	0.90[ASN][1000 genomes]
rs3130460	0.90[ASN][1000 genomes]
rs3130461	0.87[ASN][1000 genomes]
rs3130462	0.87[ASN][1000 genomes]
rs3130463	0.87[ASN][1000 genomes]
rs3130466	0.83[ASN][1000 genomes]
rs3130503	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130512	0.85[ASN][1000 genomes]
rs3130952	0.85[ASN][1000 genomes]
rs3131011	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131017	0.91[ASN][1000 genomes]
rs3132501	0.83[ASN][1000 genomes]
rs3132503	0.84[ASN][1000 genomes]
rs3132504	0.85[ASN][1000 genomes]
rs3132507	0.84[ASN][1000 genomes]
rs3132509	0.85[ASN][1000 genomes]
rs3132517	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3132538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132539	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3134789	0.88[ASN][1000 genomes]
rs4343960	0.90[ASN][1000 genomes]
rs9263761	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9263788	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	esv33699	chr6:31094845-31110011	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
15	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
16	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
17	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31105600-31110000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:31105600-31110200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:31105600-31110400	Weak transcription	Fetal Lung	lung
4	chr6:31105600-31124400	Weak transcription	Fetal Kidney	kidney
5	chr6:31105600-31124800	Weak transcription	Small Intestine	intestine
6	chr6:31105800-31110200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:31105800-31110200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:31105800-31110200	Weak transcription	Adipose Nuclei	Adipose
9	chr6:31105800-31110200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:31105800-31110200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:31105800-31110200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:31105800-31110400	Weak transcription	Primary T cells from cord blood	blood
13	chr6:31105800-31110400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:31105800-31110400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:31105800-31110400	Weak transcription	Brain Angular Gyrus	brain
16	chr6:31105800-31110400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:31105800-31110400	Weak transcription	K562	blood
18	chr6:31105800-31110400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:31105800-31110600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:31105800-31110600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:31105800-31110600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:31105800-31110600	Weak transcription	Fetal Brain Female	brain
23	chr6:31105800-31110600	Weak transcription	Osteobl	bone
24	chr6:31105800-31110800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:31105800-31110800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:31105800-31117000	Weak transcription	Brain Substantia Nigra	brain
27	chr6:31105800-31117200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr6:31105800-31117800	Weak transcription	Primary B cells from cord blood	blood
29	chr6:31105800-31121800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:31105800-31122600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:31105800-31124400	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:31105800-31124800	Weak transcription	Hela-S3	cervix
33	chr6:31105800-31125200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:31106000-31110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:31106000-31110200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:31106000-31110200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:31106000-31110200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:31106000-31110200	Weak transcription	Fetal Intestine Large	intestine
39	chr6:31106000-31110200	Weak transcription	Fetal Thymus	thymus
40	chr6:31106000-31110400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:31106000-31110400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:31106000-31110400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:31106000-31111000	Weak transcription	Colonic Mucosa	Colon
44	chr6:31106000-31111800	Weak transcription	GM12878-XiMat	blood
45	chr6:31106000-31112800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr6:31106000-31125000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:31106000-31125000	Weak transcription	Fetal Brain Male	brain
48	chr6:31106000-31125200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:31106800-31110000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr6:31107200-31110400	Weak transcription	NHLF	lung

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