Variant report

Variant	rs2003471
Chromosome Location	chr12:48124893-48124894
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48123429..48125813-chr12:48228513..48231351,2	MCF-7	breast:
2	chr12:48117242..48121350-chr12:48124704..48128284,5	MCF-7	breast:
3	chr12:48123237..48125446-chr12:48212337..48215614,3	MCF-7	breast:
4	chr12:48121475..48125710-chr12:48127578..48130124,5	MCF-7	breast:
5	chr12:48124296..48127190-chr12:48166396..48170138,3	MCF-7	breast:
6	chr12:48122622..48126569-chr12:48133427..48136331,4	K562	blood:
7	chr12:48123494..48126163-chr12:48177951..48180667,2	MCF-7	breast:
8	chr12:48115954..48117583-chr12:48123112..48125553,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000079337	Chromatin interaction
ENSG00000268069	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000111405	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10875683	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168212	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168219	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11168220	0.82[ASN][1000 genomes]
rs11830795	0.89[ASN][1000 genomes]
rs11834770	0.89[ASN][1000 genomes]
rs1235152	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12812460	0.84[ASN][1000 genomes]
rs12812960	0.94[ASN][1000 genomes]
rs12820269	0.82[ASN][1000 genomes]
rs12828238	0.86[ASN][1000 genomes]
rs2074531	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074532	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239188	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2283345	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2285830	0.89[ASN][1000 genomes]
rs3764015	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764016	0.89[ASN][1000 genomes]
rs3764018	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764019	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764020	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4505143	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4537844	0.82[ASN][1000 genomes]
rs6580635	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580636	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7133585	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726588	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7302276	0.84[ASN][1000 genomes]
rs7306556	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs757284	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967336	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967546	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7976708	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 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	chr12:48112000-48126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:48112200-48125400	Weak transcription	Fetal Thymus	thymus
4	chr12:48112200-48127000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:48112600-48128600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:48114000-48134400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:48114200-48132600	Weak transcription	Primary B cells from cord blood	blood
8	chr12:48114600-48128800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:48115200-48126200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:48115600-48133600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:48115600-48134200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:48115600-48135000	Weak transcription	Primary T cells from cord blood	blood
13	chr12:48116200-48134000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:48116800-48130200	Weak transcription	Aorta	Aorta
15	chr12:48117000-48129000	Weak transcription	Psoas Muscle	Psoas
16	chr12:48118200-48128800	Weak transcription	Fetal Intestine Small	intestine
17	chr12:48119000-48126000	Enhancers	NHDF-Ad	bronchial
18	chr12:48119200-48125000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:48119600-48125000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr12:48119800-48128600	Weak transcription	Colonic Mucosa	Colon
21	chr12:48120400-48128600	Weak transcription	NH-A	brain
22	chr12:48121400-48125800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr12:48122400-48125000	Enhancers	Fetal Muscle Trunk	muscle
24	chr12:48122400-48125000	Enhancers	Fetal Muscle Leg	muscle
25	chr12:48122600-48125000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr12:48122600-48125000	Enhancers	Fetal Stomach	stomach
27	chr12:48122800-48126400	Enhancers	Fetal Heart	heart
28	chr12:48123000-48125000	Enhancers	Pancreas	Pancrea
29	chr12:48123000-48125800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:48123000-48128400	Weak transcription	Spleen	Spleen
31	chr12:48123600-48125600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:48123600-48127000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:48123600-48128600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:48123600-48128600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:48123800-48125600	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:48123800-48128200	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:48124000-48127400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:48124200-48125600	Weak transcription	Brain Angular Gyrus	brain
39	chr12:48124200-48126800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:48124200-48127000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:48124200-48128400	Weak transcription	Fetal Kidney	kidney
42	chr12:48124200-48130000	Weak transcription	Liver	Liver
43	chr12:48124400-48125600	Weak transcription	Left Ventricle	heart
44	chr12:48124400-48125600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:48124400-48126400	Weak transcription	Right Atrium	heart
46	chr12:48124400-48129000	Weak transcription	Gastric	stomach
47	chr12:48124400-48129600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:48124600-48125600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:48124600-48125600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:48124600-48125600	Weak transcription	Brain Substantia Nigra	brain

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