Variant report

Variant	rs12220852
Chromosome Location	chr10:6133371-6133372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6132741..6135647-chr10:6244936..6248119,3	MCF-7	breast:
2	chr10:6018551..6021640-chr10:6130714..6134315,5	MCF-7	breast:
3	chr10:6133090..6135580-chr10:6163939..6166361,2	K562	blood:
4	chr10:6130983..6133585-chr10:6620139..6622430,2	K562	blood:
5	chr10:6131418..6133941-chr10:6140772..6145305,6	K562	blood:
6	chr10:6131173..6133943-chr10:6186718..6189110,2	MCF-7	breast:
7	chr10:6128513..6130219-chr10:6132306..6134990,2	MCF-7	breast:
8	chr10:6131719..6134216-chr10:6253022..6254903,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237943	Chromatin interaction
ENSG00000065675	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000134470	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10905773	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10905806	0.84[EUR][1000 genomes]
rs11256667	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256848	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11256860	0.81[ASN][1000 genomes]
rs11256879	0.81[ASN][1000 genomes]
rs12571090	0.86[ASN][1000 genomes]
rs2274358	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2274359	0.91[ASN][1000 genomes]
rs3930531	0.83[EUR][1000 genomes]
rs4747865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4749957	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7894037	0.86[ASN][1000 genomes]
rs7899110	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv894815	chr10:6108439-6161781	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1040397	chr10:6129759-6158697	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6132000-6133800	Flanking Active TSS	Dnd41	blood
2	chr10:6132200-6133400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:6132200-6133400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:6132200-6133400	Enhancers	Spleen	Spleen
5	chr10:6132200-6134000	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:6132200-6134200	Enhancers	Small Intestine	intestine
7	chr10:6132200-6134400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:6132200-6135800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr10:6132200-6138200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:6132200-6139200	Weak transcription	Gastric	stomach
11	chr10:6132400-6133400	Enhancers	Fetal Intestine Large	intestine
12	chr10:6132400-6133400	Enhancers	Fetal Muscle Trunk	muscle
13	chr10:6132400-6133400	Enhancers	Fetal Muscle Leg	muscle
14	chr10:6132400-6133800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:6132400-6134000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr10:6132400-6134000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr10:6132400-6134200	Enhancers	Brain Cingulate Gyrus	brain
18	chr10:6132400-6135000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr10:6132400-6135400	Enhancers	Primary B cells from cord blood	blood
20	chr10:6132400-6139000	Weak transcription	Esophagus	oesophagus
21	chr10:6132400-6139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr10:6132400-6139200	Weak transcription	Aorta	Aorta
23	chr10:6132400-6139600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr10:6132600-6133600	Enhancers	Fetal Stomach	stomach
25	chr10:6132600-6133600	Enhancers	Fetal Thymus	thymus
26	chr10:6132600-6133800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:6132600-6133800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:6132600-6133800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr10:6132600-6134000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr10:6132600-6134000	Enhancers	Colon Smooth Muscle	Colon
31	chr10:6132600-6134000	Enhancers	Ovary	ovary
32	chr10:6132600-6134200	Enhancers	H1 Cell Line	embryonic stem cell
33	chr10:6132600-6134200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr10:6132600-6134200	Enhancers	Brain Germinal Matrix	brain
35	chr10:6132600-6134400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr10:6132600-6134400	Enhancers	Liver	Liver
37	chr10:6132600-6134600	Enhancers	Duodenum Mucosa	Duodenum
38	chr10:6132600-6134800	Enhancers	Primary T cells from cord blood	blood
39	chr10:6132600-6134800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr10:6132600-6135000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:6132600-6135000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr10:6132600-6135000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr10:6132600-6135200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr10:6132600-6137600	Weak transcription	HSMM	muscle
45	chr10:6132600-6138600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr10:6132600-6139000	Weak transcription	Colonic Mucosa	Colon
47	chr10:6132600-6139200	Weak transcription	Pancreas	Pancrea
48	chr10:6132800-6133400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr10:6132800-6133400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:6132800-6133400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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