Variant report

Variant	rs6580806
Chromosome Location	chr12:51599339-51599340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51476335..51478466-chr12:51598022..51600514,2	K562	blood:
2	chr12:51597757..51600269-chr12:51632271..51633974,2	MCF-7	breast:
3	chr12:51475917..51477628-chr12:51596948..51599509,2	MCF-7	breast:
4	chr12:51596681..51599666-chr12:51600800..51605686,4	MCF-7	breast:
5	chr12:51591743..51595531-chr12:51598631..51600662,3	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000184271	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10735833	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs10783420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4076884	0.85[EUR][1000 genomes]
rs4077093	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580805	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6580810	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6580811	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7311832	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs7398898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv558876	chr12:51591367-51612730	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6580806	RARG	cis	cerebellum	SCAN
rs6580806	POU6F1	cis	cerebellum	SCAN
rs6580806	KRT83	cis	parietal	SCAN
rs6580806	TMEM106C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51567400-51610600	Weak transcription	Right Atrium	heart
2	chr12:51581400-51600400	Weak transcription	Psoas Muscle	Psoas
3	chr12:51581400-51610200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:51581800-51610600	Weak transcription	Colonic Mucosa	Colon
5	chr12:51582200-51608000	Weak transcription	NHLF	lung
6	chr12:51582400-51600000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:51582400-51600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:51583400-51602400	Weak transcription	Fetal Brain Male	brain
9	chr12:51584400-51610800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:51585000-51610200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:51585000-51610800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:51585400-51610200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:51585800-51601400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:51585800-51610400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:51586000-51610200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:51586400-51610200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:51590800-51610400	Weak transcription	HSMMtube	muscle
18	chr12:51592200-51602400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:51592400-51610200	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:51592400-51610600	Weak transcription	Pancreas	Pancrea
21	chr12:51592400-51610800	Weak transcription	Esophagus	oesophagus
22	chr12:51592800-51610200	Weak transcription	Right Ventricle	heart
23	chr12:51592800-51610400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:51593200-51610200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:51593600-51601200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:51594200-51601200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:51594400-51610400	Weak transcription	Liver	Liver
28	chr12:51595200-51610800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:51595600-51610400	Weak transcription	NH-A	brain
30	chr12:51596000-51599400	Strong transcription	Fetal Stomach	stomach
31	chr12:51596000-51610200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:51596600-51604200	Weak transcription	Small Intestine	intestine
33	chr12:51596800-51605600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:51597400-51599600	Strong transcription	Aorta	Aorta
35	chr12:51597400-51610200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:51597400-51610200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:51597400-51611000	Weak transcription	Primary T cells from cord blood	blood
38	chr12:51597600-51610400	Weak transcription	Fetal Lung	lung
39	chr12:51597800-51610000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:51597800-51610000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:51597800-51610400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:51598000-51600400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:51598000-51600400	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:51598000-51604400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:51598000-51610200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:51598000-51610200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:51598000-51610200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:51598000-51610400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr12:51598000-51610400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr12:51598200-51599400	Enhancers	Placenta	Placenta

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