Variant report

Variant	rs12228199
Chromosome Location	chr12:64256568-64256569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64254946..64256892-chr12:64282588..64284962,2	MCF-7	breast:
2	chr12:64254678..64258025-chr12:64259314..64262432,3	MCF-7	breast:
3	chr12:64248653..64250464-chr12:64256025..64258029,2	MCF-7	breast:
4	chr12:64240146..64242509-chr12:64254956..64256783,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11175184	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175185	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175188	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175189	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175197	0.96[ASN][1000 genomes]
rs11833808	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11835034	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229790	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579795	0.88[YRI][hapmap]
rs17099866	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2335884	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35143986	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072758	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55642517	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55655348	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55760535	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55907605	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55930806	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56028204	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56080061	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56264182	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58424013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59063572	0.85[EUR][1000 genomes]
rs60031756	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6581509	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581510	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66856673	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67401817	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67684483	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67830727	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67880496	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67892056	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67993208	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68188132	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7136130	1.00[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7294327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7301437	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302672	0.83[CEU][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7304340	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305893	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307108	0.83[CEU][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308850	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]
rs7310327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7310329	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7310575	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311611	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73313479	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73315321	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73315365	0.98[ASN][1000 genomes]
rs7953208	0.84[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv1810729	chr12:64234926-64268005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
5	esv1797043	chr12:64237504-64256568	Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
6	esv1833454	chr12:64237504-64264837	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
7	esv1803717	chr12:64250221-64261249	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12228199	SRGAP1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64241000-64257200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:64241000-64261200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:64241000-64268800	Weak transcription	Lung	lung
4	chr12:64241000-64278800	Weak transcription	Fetal Stomach	stomach
5	chr12:64243400-64263000	Weak transcription	NHEK	skin
6	chr12:64244000-64263600	Weak transcription	Fetal Lung	lung
7	chr12:64246200-64286400	Weak transcription	Fetal Brain Female	brain
8	chr12:64247800-64257400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:64247800-64268200	Weak transcription	Fetal Brain Male	brain
10	chr12:64250200-64287200	Weak transcription	Aorta	Aorta
11	chr12:64254200-64259200	Enhancers	Fetal Intestine Large	intestine
12	chr12:64254400-64257000	Enhancers	HepG2	liver
13	chr12:64254400-64257400	Enhancers	Stomach Mucosa	stomach
14	chr12:64254400-64257400	Enhancers	NHDF-Ad	bronchial
15	chr12:64255000-64258600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:64255200-64257000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:64255200-64258000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr12:64255200-64258600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr12:64255200-64259000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:64255400-64257400	Enhancers	Liver	Liver
21	chr12:64255400-64257800	Enhancers	HMEC	breast
22	chr12:64255400-64258600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:64255800-64256800	Enhancers	Brain Anterior Caudate	brain
24	chr12:64255800-64256800	Enhancers	Fetal Heart	heart
25	chr12:64255800-64258400	Enhancers	Osteobl	bone
26	chr12:64256000-64256600	Enhancers	Brain Hippocampus Middle	brain
27	chr12:64256000-64256600	Enhancers	NHLF	lung
28	chr12:64256000-64256800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:64256000-64256800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr12:64256000-64256800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:64256000-64256800	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr12:64256000-64256800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr12:64256000-64256800	Enhancers	HSMM	muscle
34	chr12:64256000-64256800	Enhancers	HUVEC	blood vessel
35	chr12:64256000-64257000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr12:64256000-64257000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:64256000-64257000	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr12:64256000-64257000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:64256000-64257000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr12:64256000-64257000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:64256000-64257000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr12:64256000-64257000	Enhancers	NH-A	brain
43	chr12:64256000-64257200	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:64256000-64257200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:64256000-64257400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:64256000-64257800	Enhancers	Small Intestine	intestine
47	chr12:64256200-64256600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr12:64256200-64256600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:64256200-64256600	Enhancers	Brain Substantia Nigra	brain
50	chr12:64256200-64256600	Active TSS	Rectal Mucosa Donor 29	rectum

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