Variant report

Variant	rs6580636
Chromosome Location	chr12:48116633-48116634
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:48115854-48116651	MCF-7	breast:	n/a	n/a
2	CTCF	chr12:48116560-48116710	Caco-2	colon:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48115954..48117583-chr12:48123112..48125553,2	K562	blood:
2	chr12:48116185..48118625-chr12:48317978..48320277,2	K562	blood:
3	chr12:48097267..48105309-chr12:48111877..48120917,8	MCF-7	breast:
4	chr12:48110039..48113166-chr12:48116140..48121059,8	MCF-7	breast:
5	chr12:48115974..48118719-chr12:48231014..48233815,2	K562	blood:
6	chr12:48111138..48113167-chr12:48114510..48117991,4	K562	blood:
7	chr12:48111480..48113167-chr12:48115489..48118997,3	K562	blood:
8	chr12:48116074..48118098-chr12:48152028..48153707,2	K562	blood:
9	chr12:48115323..48118041-chr12:48153022..48154829,2	MCF-7	breast:
10	chr12:48113943..48116894-chr12:48118403..48120820,3	K562	blood:

No data

Variant related genes	Relation type
ENDOU	TF binding region
ENSG00000111405	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000257433	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10875683	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168187	0.86[ASN][1000 genomes]
rs11168194	0.81[JPT][hapmap]
rs11168212	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168219	0.86[ASN][1000 genomes]
rs11168220	0.82[ASN][1000 genomes]
rs11830795	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11834770	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1235152	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812460	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12812960	0.94[ASN][1000 genomes]
rs12819759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12820269	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12828238	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2003471	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238144	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs2239188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283345	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285830	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3764015	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764016	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3764018	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764019	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4505143	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4537844	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133585	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726588	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7302276	0.94[ASN][1000 genomes]
rs7306556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757284	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
6	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48102800-48125000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:48111400-48124000	Weak transcription	Gastric	stomach
3	chr12:48111800-48117000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:48112000-48117000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:48112000-48118200	Weak transcription	Fetal Intestine Large	intestine
6	chr12:48112000-48118400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:48112000-48120000	Weak transcription	Fetal Lung	lung
8	chr12:48112000-48120000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:48112000-48122800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:48112000-48123000	Weak transcription	Pancreas	Pancrea
11	chr12:48112000-48126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:48112200-48117200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:48112200-48118600	Weak transcription	Stomach Mucosa	stomach
14	chr12:48112200-48119000	Weak transcription	Colonic Mucosa	Colon
15	chr12:48112200-48119200	Weak transcription	GM12878-XiMat	blood
16	chr12:48112200-48125400	Weak transcription	Fetal Thymus	thymus
17	chr12:48112200-48127000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:48112600-48116800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:48112600-48119000	Weak transcription	Right Atrium	heart
20	chr12:48112600-48119200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:48112600-48119400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:48112600-48122200	Weak transcription	Spleen	Spleen
23	chr12:48112600-48128600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:48112800-48119600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:48113000-48123400	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:48113200-48117800	Strong transcription	Liver	Liver
27	chr12:48113400-48119400	Weak transcription	Adipose Nuclei	Adipose
28	chr12:48113600-48118600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr12:48114000-48120800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:48114000-48134400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:48114200-48122200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:48114200-48132600	Weak transcription	Primary B cells from cord blood	blood
33	chr12:48114400-48117400	Strong transcription	Fetal Stomach	stomach
34	chr12:48114600-48117200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:48114600-48117800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr12:48114600-48128800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:48114800-48117000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr12:48115000-48117800	Enhancers	Brain Anterior Caudate	brain
39	chr12:48115200-48126200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:48115400-48117200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:48115400-48117600	Enhancers	Brain Substantia Nigra	brain
42	chr12:48115400-48117800	Weak transcription	Fetal Intestine Small	intestine
43	chr12:48115600-48117400	Enhancers	Brain Hippocampus Middle	brain
44	chr12:48115600-48119000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:48115600-48119400	Weak transcription	HSMM	muscle
46	chr12:48115600-48123800	Weak transcription	Thymus	Thymus
47	chr12:48115600-48133600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:48115600-48134200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:48115600-48135000	Weak transcription	Primary T cells from cord blood	blood
50	chr12:48115800-48117000	Weak transcription	NHDF-Ad	bronchial

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