Variant report

Variant	rs12379
Chromosome Location	chr12:51442944-51442945
allele	C/T
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:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51421719..51422616-chr12:51442889..51443788,2	MCF-7	breast:
2	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
3	chr12:51440622..51443141-chr12:51753837..51755674,2	MCF-7	breast:
4	chr12:51440322..51443098-chr12:51662230..51665433,4	K562	blood:
5	chr12:51440588..51444188-chr12:51475693..51478745,10	K562	blood:
6	chr12:1100037..1100656-chr12:51442773..51443406,2	Hela-S3	cervix:
7	chr12:51440271..51447226-chr12:51475135..51479930,16	MCF-7	breast:
8	chr12:51440439..51443022-chr12:51565659..51567306,3	K562	blood:
9	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
10	chr12:51439067..51445190-chr12:51449547..51456560,11	K562	blood:
11	chr12:51421116..51422954-chr12:51442627..51444321,2	K562	blood:
12	chr12:51157036..51159803-chr12:51442013..51443781,2	K562	blood:
13	chr12:51440642..51443592-chr12:51616961..51619958,3	MCF-7	breast:
14	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
15	chr12:51441202..51443113-chr12:51468336..51471322,2	K562	blood:
16	chr12:51440743..51444863-chr12:51448295..51453075,7	MCF-7	breast:
17	chr12:51440639..51443821-chr12:51630707..51634068,3	K562	blood:
18	chr12:51399373..51401239-chr12:51441069..51443548,3	MCF-7	breast:
19	chr12:51441021..51443304-chr12:51610017..51612719,2	MCF-7	breast:
20	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
21	chr12:51440554..51443122-chr12:51610984..51612842,2	K562	blood:
22	chr12:51441811..51444855-chr12:51447426..51450145,3	K562	blood:
23	chr12:51440782..51445752-chr12:51631445..51635429,5	MCF-7	breast:
24	chr12:51442131..51443654-chr12:51632359..51634023,2	MCF-7	breast:
25	chr12:51441619..51444815-chr12:51631402..51636504,5	K562	blood:
26	chr12:51440588..51444188-chr12:51475774..51478819,7	K562	blood:
27	chr12:51440852..51445521-chr12:51475730..51478507,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184271	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000250132	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000269339	Chromatin interaction
ENSG00000139629	Chromatin interaction
ENSG00000082805	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10783409	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10783413	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876127	0.91[ASN][1000 genomes]
rs10876129	0.91[ASN][1000 genomes]
rs10876130	0.85[CHB][hapmap]
rs10876131	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10876132	0.84[ASN][1000 genomes]
rs10876136	1.00[CHB][hapmap]
rs10876138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs11169657	0.84[ASN][1000 genomes]
rs11169695	0.85[ASN][1000 genomes]
rs11169710	1.00[CHB][hapmap]
rs12424509	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12427345	0.91[ASN][1000 genomes]
rs1466579	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1486014	0.91[ASN][1000 genomes]
rs15756	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1632791	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs17125111	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2010630	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2029145	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2029146	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs224448	0.84[ASN][1000 genomes]
rs224572	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2730655	0.89[EUR][1000 genomes]
rs370462	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs3759405	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427020	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4438107	1.00[CHB][hapmap]
rs4768970	0.82[EUR][1000 genomes]
rs4991549	0.83[EUR][1000 genomes]
rs55874804	0.91[ASN][1000 genomes]
rs61934800	0.91[ASN][1000 genomes]
rs6580782	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6580785	1.00[CHB][hapmap]
rs6580787	0.83[EUR][1000 genomes]
rs6580788	1.00[CHB][hapmap]
rs6580791	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs706805	0.84[ASN][1000 genomes]
rs7135399	0.91[ASN][1000 genomes]
rs7136960	0.91[ASN][1000 genomes]
rs7953867	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7971308	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976431	0.91[ASN][1000 genomes]
rs7977740	0.84[ASN][1000 genomes]
rs901313	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9739342	0.91[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12379	CSAD	cis	parietal	SCAN
rs12379	KRT79	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51441000-51443200	Active TSS	A549	lung
2	chr12:51441000-51443400	Active TSS	GM12878-XiMat	blood
3	chr12:51441000-51443600	Active TSS	Psoas Muscle	Psoas
4	chr12:51441200-51443000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr12:51441200-51443000	Active TSS	Fetal Kidney	kidney
6	chr12:51441200-51443000	Active TSS	Gastric	stomach
7	chr12:51441200-51443200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:51441200-51443200	Active TSS	Right Ventricle	heart
9	chr12:51441200-51443200	Active TSS	K562	blood
10	chr12:51441400-51443000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr12:51441400-51443000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:51441400-51443000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:51441400-51443000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:51441400-51443000	Active TSS	Left Ventricle	heart
15	chr12:51441400-51443000	Active TSS	Lung	lung
16	chr12:51441400-51443000	Active TSS	Pancreas	Pancrea
17	chr12:51441400-51443200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr12:51441400-51443200	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr12:51441400-51443200	Active TSS	Ovary	ovary
20	chr12:51441400-51443200	Active TSS	Right Atrium	heart
21	chr12:51441400-51443400	Active TSS	Esophagus	oesophagus
22	chr12:51441400-51443400	Active TSS	Fetal Intestine Large	intestine
23	chr12:51441600-51443000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:51441600-51443000	Active TSS	Fetal Muscle Trunk	muscle
25	chr12:51441600-51443000	Active TSS	Placenta	Placenta
26	chr12:51441600-51443000	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr12:51441600-51443200	Active TSS	Fetal Intestine Small	intestine
28	chr12:51441600-51443400	Active TSS	Stomach Mucosa	stomach
29	chr12:51442200-51443000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr12:51442200-51443000	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr12:51442200-51443000	Bivalent/Poised TSS	HepG2	liver
32	chr12:51442200-51443200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr12:51442200-51443200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr12:51442200-51443400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:51442200-51443600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:51442200-51443600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr12:51442400-51443000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:51442400-51443000	Flanking Active TSS	Colonic Mucosa	Colon
39	chr12:51442400-51443000	Flanking Active TSS	Fetal Brain Male	brain
40	chr12:51442400-51443000	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr12:51442400-51443200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr12:51442400-51443200	Flanking Active TSS	Osteobl	bone
43	chr12:51442400-51443400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:51442400-51443400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr12:51442400-51443400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr12:51442400-51443400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr12:51442400-51443400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:51442400-51443400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:51442400-51443400	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr12:51442400-51443400	Flanking Active TSS	Liver	Liver

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