Variant report

Variant	rs12563229
Chromosome Location	chr1:93204768-93204769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93203847..93205464-chr1:93207057..93209940,2	K562	blood:
2	chr1:93199006..93201048-chr1:93203256..93205414,2	K562	blood:
3	chr1:93204366..93207086-chr1:93298267..93300832,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122406	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10127800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12564537	1.00[ASN][1000 genomes]
rs12566186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13374365	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391198	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28550182	1.00[ASN][1000 genomes]
rs55995837	1.00[ASN][1000 genomes]
rs56185219	1.00[ASN][1000 genomes]
rs59925050	1.00[ASN][1000 genomes]
rs74101363	1.00[ASN][1000 genomes]
rs7548287	1.00[ASN][1000 genomes]
rs9803725	1.00[AMR][1000 genomes];1.00[EUR][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	esv1802611	chr1:93090476-93219907	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv997898	chr1:93167128-93228156	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	esv3340706	chr1:93187980-93207933	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv871263	chr1:93196273-93248228	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3392576	chr1:93204608-93204882	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93098400-93205400	Weak transcription	NHLF	lung
2	chr1:93123600-93213400	Weak transcription	Gastric	stomach
3	chr1:93155800-93213400	Weak transcription	Lung	lung
4	chr1:93186600-93205600	Weak transcription	Ovary	ovary
5	chr1:93186800-93213400	Weak transcription	K562	blood
6	chr1:93188400-93205400	Weak transcription	Small Intestine	intestine
7	chr1:93189000-93213400	Weak transcription	Fetal Lung	lung
8	chr1:93189400-93206000	Weak transcription	Brain Anterior Caudate	brain
9	chr1:93190000-93221800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:93190200-93220000	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:93191200-93221600	Weak transcription	Fetal Intestine Large	intestine
12	chr1:93192400-93221200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:93192400-93226400	Weak transcription	Esophagus	oesophagus
14	chr1:93193000-93223800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:93193600-93213200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:93194600-93207400	Weak transcription	Osteobl	bone
17	chr1:93194600-93218000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:93195000-93218000	Weak transcription	NHEK	skin
19	chr1:93196200-93213400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:93197600-93210800	Weak transcription	Placenta	Placenta
21	chr1:93198000-93205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:93198200-93205000	Weak transcription	Primary B cells from cord blood	blood
23	chr1:93198200-93209000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:93199400-93204800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:93199600-93210600	Weak transcription	Fetal Stomach	stomach
26	chr1:93199600-93211200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:93199600-93211200	Weak transcription	Left Ventricle	heart
28	chr1:93199600-93212800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:93200200-93207800	Weak transcription	Fetal Intestine Small	intestine
30	chr1:93200200-93224000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:93201000-93205000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr1:93201000-93205000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:93201000-93205800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:93201000-93208600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:93201000-93208600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:93201000-93210400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:93201000-93210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:93201000-93211000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:93201000-93211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:93201000-93211600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:93201000-93213400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:93201000-93213400	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:93201000-93218200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:93201000-93218200	Weak transcription	NH-A	brain
45	chr1:93201000-93220000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:93202200-93206800	Weak transcription	HSMM	muscle
47	chr1:93202200-93208400	Weak transcription	Monocytes-CD14+_RO01746	blood

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