Variant report

Variant	rs7308850
Chromosome Location	chr12:64215629-64215630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:64215547-64216043	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:64215589-64215940	ProgFib	skin:	n/a	n/a
3	NRF1	chr12:64215516-64215838	GM12878	blood:	n/a	chr12:64215675-64215689 chr12:64215678-64215689 chr12:64215684-64215695
4	POLR2A	chr12:64215433-64215961	GM19193	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:64215611-64215661	HNPCEpiC	eye:	n/a
2	chr12:64215611-64215661	HCPEpiC	choroid plexus:	n/a
3	chr12:64215611-64215661	HUVEC	blood vessel:	n/a
4	chr12:64215611-64215661	HMEC	breast:	n/a
5	chr12:64215611-64215661	NB4	blood:	n/a
6	chr12:64215611-64215661	ovcar-3	ovarian:	n/a
7	chr12:64215611-64215661	NH-A	brain:	n/a
8	chr12:64215611-64215661	T-47D	breast:	n/a
9	chr12:64215611-64215661	GM06990	blood:	n/a
10	chr12:64215611-64215661	Caco-2	colon:	n/a
11	chr12:64215611-64215661	HCT-116	colon:	n/a
12	chr12:64215611-64215661	SAEC	small airway:	n/a
13	chr12:64215611-64215661	NHDF-neo	bronchial:	n/a
14	chr12:64215611-64215661	Hepatocyte	liver:	n/a
15	chr12:64215611-64215661	HEK293	kidney:	embryo
16	chr12:64215611-64215661	MCF-7	breast:	n/a
17	chr12:64215611-64215661	IMR90	lung:	fetal
18	chr12:64215611-64215661	PFSK-1	brain:	n/a
19	chr12:64215611-64215661	AG04450	lung:	fetal
20	chr12:64215611-64215661	HIPEpiC	eye:	n/a
21	chr12:64215611-64215661	GM19239	blood:	n/a
22	chr12:64215611-64215661	H1-hESC	embryonic stem cell:	embryo
23	chr12:64215611-64215661	CMK	blood:	n/a
24	chr12:64215611-64215661	GM12892	blood:	n/a
25	chr12:64215611-64215661	SK-N-SH	brain:	n/a
26	chr12:64215611-64215661	GM12878	blood:	n/a
27	chr12:64215611-64215661	PrEC	prostate:	n/a
28	chr12:64215611-64215661	BJ	skin:	n/a
29	chr12:64215611-64215661	PANC-1	pancreas:	n/a
30	chr12:64215611-64215661	AG10803	skin:	n/a
31	chr12:64215611-64215661	SK-N-SH_RA	brain:	n/a
32	chr12:64215611-64215661	HRPEpiC	eye:	n/a
33	chr12:64215611-64215661	HRE	kidney:	n/a
34	chr12:64215611-64215661	BE2_C	brain:	n/a
35	chr12:64215611-64215661	HAEpiC	amniotic membrane:	n/a
36	chr12:64215611-64215661	SKMC	muscle:	n/a
37	chr12:64215611-64215661	NT2-D1	testis:	n/a
38	chr12:64215611-64215661	HCF	heart:	n/a
39	chr12:64215611-64215661	AG09319	gingival:	n/a
40	chr12:64215611-64215661	A549	lung:	n/a
41	chr12:64215611-64215661	LNCaP	prostate:	n/a
42	chr12:64215611-64215661	U87	brain:	n/a
43	chr12:64215611-64215661	AG04449	skin:	fetal
44	chr12:64215611-64215661	Jurkat	blood:	n/a
45	chr12:64215611-64215661	RPTEC	kidney:	n/a
46	chr12:64215611-64215661	HPAEpiC	pulmonary alveolar:	n/a
47	chr12:64215611-64215661	HL-60	blood:	n/a
48	chr12:64215611-64215661	HRCEpiC	kidney:	n/a
49	chr12:64215611-64215661	K562	blood:	n/a
50	chr12:64215611-64215661	AoSMC	blood vessel:	n/a

No data

Variant related genes	Relation type
PABPC1P4	TF binding region
PABPC1P4	CpG island

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10506464	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11175184	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11175185	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11175188	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11175189	0.89[ASW][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11175197	0.82[ASN][1000 genomes]
rs11833808	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11835034	0.94[ASW][hapmap];0.83[CHB][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12228199	0.89[ASW][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229790	0.83[ASN][1000 genomes]
rs12579795	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17099866	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2335884	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35143986	0.89[ASW][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs4072758	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4497499	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs55642517	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55655348	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55760535	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55907605	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55930806	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56028204	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56080061	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56264182	0.96[ASN][1000 genomes]
rs58424013	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59063572	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60031756	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581509	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6581510	0.83[ASN][1000 genomes]
rs66856673	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67401817	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67684483	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67830727	0.82[ASN][1000 genomes]
rs67880496	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67892056	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67993208	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68188132	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136130	0.89[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7294327	0.83[CHB][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301437	0.82[ASN][1000 genomes]
rs7302672	0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7304340	0.89[ASW][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs7305893	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7307108	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310327	0.89[ASW][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7310329	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310575	0.86[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7311353	0.87[EUR][1000 genomes]
rs7311611	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73313479	0.96[ASN][1000 genomes]
rs73315321	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73315365	0.84[ASN][1000 genomes]
rs7953208	0.83[ASW][hapmap];0.87[CHB][hapmap];0.83[ASN][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	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv746	chr12:64189444-64234966	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7308850	SRGAP1	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64203400-64215800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:64215200-64215800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:64215200-64216000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:64215200-64216000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:64215200-64216400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:64215200-64216400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr12:64215200-64216600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:64215400-64215800	Active TSS	Primary B cells from cord blood	blood
9	chr12:64215400-64215800	Active TSS	Primary hematopoietic stem cells	blood
10	chr12:64215400-64215800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr12:64215400-64215800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:64215400-64215800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
13	chr12:64215400-64215800	Active TSS	Left Ventricle	heart
14	chr12:64215400-64215800	Active TSS	Placenta Amnion	Placenta Amnion
15	chr12:64215400-64215800	Active TSS	HSMM	muscle
16	chr12:64215400-64215800	Active TSS	NH-A	brain
17	chr12:64215400-64215800	Active TSS	NHEK	skin
18	chr12:64215400-64216000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr12:64215400-64216000	Active TSS	Primary T cells from cord blood	blood
20	chr12:64215400-64216000	Bivalent/Poised TSS	Primary T cells fromperipheralblood	blood
21	chr12:64215400-64216000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:64215400-64216000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:64215400-64216000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:64215400-64216000	Active TSS	Aorta	Aorta
25	chr12:64215400-64216000	Active TSS	Liver	Liver
26	chr12:64215400-64216000	Active TSS	Esophagus	oesophagus
27	chr12:64215400-64216000	Active TSS	Fetal Brain Female	brain
28	chr12:64215400-64216000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr12:64215400-64216000	Bivalent/Poised TSS	Fetal Stomach	stomach
30	chr12:64215400-64216000	Active TSS	Right Atrium	heart
31	chr12:64215400-64216000	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr12:64215400-64216000	Active TSS	Thymus	Thymus
33	chr12:64215400-64216000	Active TSS	Osteobl	bone
34	chr12:64215400-64216200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:64215400-64216200	Active TSS	Brain Hippocampus Middle	brain
36	chr12:64215400-64216200	Active TSS	Colon Smooth Muscle	Colon
37	chr12:64215400-64216200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr12:64215400-64216200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
39	chr12:64215400-64216200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
40	chr12:64215400-64216200	Active TSS	Fetal Kidney	kidney
41	chr12:64215400-64216200	Active TSS	Ovary	ovary
42	chr12:64215400-64216200	Active TSS	Rectal Smooth Muscle	rectum
43	chr12:64215400-64216400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:64215400-64216400	Active TSS	Brain Anterior Caudate	brain
45	chr12:64215400-64216400	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr12:64215400-64216400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr12:64215400-64216400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
48	chr12:64215400-64216400	Active TSS	Stomach Smooth Muscle	stomach
49	chr12:64215400-64216400	Active TSS	NHLF	lung
50	chr12:64215400-64216600	Active TSS	Muscle Satellite Cultured Cells	--

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