Variant report

Variant	rs7308505
Chromosome Location	chr12:56328699-56328700
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56326218..56328799-chr12:56389598..56392484,2	K562	blood:
2	chr12:56208117..56217611-chr12:56318345..56328982,45	MCF-7	breast:
3	chr12:56318132..56330507-chr12:56363672..56369798,22	MCF-7	breast:
4	chr12:56325939..56329017-chr12:56389529..56391723,3	K562	blood:
5	chr12:56217992..56226798-chr12:56311494..56331042,68	MCF-7	breast:
6	chr12:56217492..56232243-chr12:56318854..56330686,48	MCF-7	breast:
7	chr12:56225390..56228065-chr12:56328678..56330910,3	K562	blood:
8	chr12:56326452..56329346-chr12:56360017..56362575,2	K562	blood:
9	chr12:56326233..56328752-chr12:56399282..56401795,2	MCF-7	breast:
10	chr12:56121086..56122985-chr12:56327062..56330070,3	MCF-7	breast:
11	chr12:56319350..56329795-chr12:56348492..56353182,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111540	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000123353	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10128982	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1052206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747760	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783774	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783775	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171688	0.93[AFR][1000 genomes]
rs11171743	1.00[YRI][hapmap]
rs1136082	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12298127	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12320176	1.00[YRI][hapmap]
rs12824144	1.00[YRI][hapmap]
rs12827688	1.00[YRI][hapmap]
rs1681070	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1701698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1701699	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2101718	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4414258	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61956428	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581087	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705711	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs705715	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7068	1.00[YRI][hapmap]
rs7135133	0.81[EUR][1000 genomes]
rs7297871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302957	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7312870	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs772461	0.93[AFR][1000 genomes]
rs772462	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs772468	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs772473	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs772475	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs772700	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772704	0.94[CEU][hapmap]
rs9739192	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9739196	0.88[EUR][1000 genomes];0.83[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7308505	SDR9C7	cis	cerebellum	SCAN
rs7308505	LARP4	cis	parietal	SCAN
rs7308505	GLS2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56325000-56330200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
2	chr12:56326000-56330400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
3	chr12:56326200-56330400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
4	chr12:56326400-56328800	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr12:56326400-56329400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
6	chr12:56326400-56330000	Transcr. at gene 5' and 3'	NHEK	skin
7	chr12:56326400-56331800	Weak transcription	Gastric	stomach
8	chr12:56326400-56345000	Weak transcription	Ovary	ovary
9	chr12:56326600-56328800	Enhancers	Placenta	Placenta
10	chr12:56326600-56329600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:56326600-56329600	Weak transcription	Left Ventricle	heart
12	chr12:56326800-56328800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:56326800-56328800	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr12:56326800-56328800	Enhancers	Small Intestine	intestine
15	chr12:56326800-56329000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:56326800-56329200	Weak transcription	Brain Anterior Caudate	brain
17	chr12:56326800-56329200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:56326800-56329200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:56326800-56329600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:56326800-56333600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:56326800-56333800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:56326800-56333800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:56326800-56333800	Weak transcription	K562	blood
24	chr12:56326800-56334000	Weak transcription	Lung	lung
25	chr12:56326800-56335800	Weak transcription	Aorta	Aorta
26	chr12:56327000-56328800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:56327000-56329200	Enhancers	NHLF	lung
28	chr12:56327000-56330200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:56327000-56330200	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:56327000-56333600	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:56327000-56333800	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:56327200-56328800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:56327200-56329200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:56327200-56329200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:56327200-56329200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:56327200-56329200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:56327200-56329200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:56327200-56330000	Enhancers	NHDF-Ad	bronchial
39	chr12:56327400-56330000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:56327600-56328800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:56327600-56329000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:56327600-56329200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:56327600-56329200	Weak transcription	NH-A	brain
44	chr12:56327600-56329600	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr12:56327600-56330000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:56327600-56331200	Weak transcription	HSMMtube	muscle
47	chr12:56327600-56331400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:56327600-56333200	Weak transcription	Stomach Mucosa	stomach
49	chr12:56327600-56333400	Weak transcription	HSMM	muscle
50	chr12:56327600-56333600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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