Variant report

Variant	rs6580706
Chromosome Location	chr12:49673551-49673552
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49670426..49673698-chr12:49680662..49684493,5	K562	blood:
2	chr12:49448441..49451741-chr12:49671827..49675031,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1QL4-3	chr12:49672836-49674483	ENSG00000250773
2	lnc-C1QL4-3	chr12:49672836-49674498	ENSG00000257960

Variant related genes	Relation type
ENSG00000167548	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11168963	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs7975527	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
2	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:49665400-49673800	Weak transcription	Fetal Kidney	kidney
4	chr12:49667600-49673600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:49668000-49673600	Weak transcription	Fetal Lung	lung
6	chr12:49668000-49673800	Weak transcription	Adipose Nuclei	Adipose
7	chr12:49668000-49676000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:49668000-49676000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:49668000-49678000	Weak transcription	Brain Germinal Matrix	brain
10	chr12:49668400-49673800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:49668400-49673800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:49668400-49676200	Weak transcription	NHLF	lung
13	chr12:49668600-49676000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:49668600-49682400	Weak transcription	HMEC	breast
15	chr12:49668800-49675200	Weak transcription	Spleen	Spleen
16	chr12:49669000-49674200	Weak transcription	Primary B cells from cord blood	blood
17	chr12:49669000-49676200	Weak transcription	HSMM	muscle
18	chr12:49669000-49676400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:49671400-49676000	Weak transcription	HSMMtube	muscle
20	chr12:49671400-49676200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:49671600-49673800	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:49671800-49677600	Weak transcription	Hela-S3	cervix
23	chr12:49672200-49673600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:49672200-49676400	Weak transcription	NHEK	skin
25	chr12:49672800-49674600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:49673200-49673600	Enhancers	Gastric	stomach
27	chr12:49673200-49673600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr12:49673200-49674000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:49673200-49674000	Enhancers	Brain Cingulate Gyrus	brain
30	chr12:49673200-49674000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr12:49673200-49674200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr12:49673200-49674200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr12:49673200-49674200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr12:49673400-49673600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:49673400-49673600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:49673400-49673600	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr12:49673400-49673600	Enhancers	Duodenum Mucosa	Duodenum
38	chr12:49673400-49673600	Enhancers	Esophagus	oesophagus
39	chr12:49673400-49673600	Enhancers	Left Ventricle	heart
40	chr12:49673400-49673600	Enhancers	Lung	lung
41	chr12:49673400-49673800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:49673400-49673800	Enhancers	Fetal Brain Female	brain
43	chr12:49673400-49673800	Enhancers	NH-A	brain
44	chr12:49673400-49674000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr12:49673400-49674000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr12:49673400-49674000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:49673400-49674000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:49673400-49674000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:49673400-49674000	Enhancers	H9 Cell Line	embryonic stem cell
50	chr12:49673400-49674000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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