Variant report

Variant	rs12567930
Chromosome Location	chr1:91800946-91800947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:91786405..91788910-chr1:91799387..91801097,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12562039	0.91[AMR][1000 genomes]
rs12562097	0.80[AMR][1000 genomes]
rs12564415	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12566911	0.80[AMR][1000 genomes]
rs12567679	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs12729858	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12746156	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12756869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12757442	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12759453	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12760267	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs17131418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1974253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2099749	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28395174	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34105527	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34507721	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34600283	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34744207	0.80[AMR][1000 genomes]
rs34809593	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34840774	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35081855	0.91[AMR][1000 genomes]
rs35462750	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4248874	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4658210	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4658215	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66730201	0.93[AMR][1000 genomes]
rs920469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv1800676	chr1:91722083-91854389	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv1796351	chr1:91722083-91872374	Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1006022	chr1:91768640-91831196	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv871685	chr1:91774458-91849219	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv546806	chr1:91780408-91875505	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv437904	chr1:91790876-91801207	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv519110	chr1:91794248-91800946	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12567930	ABCA4	cis	parietal	SCAN
rs12567930	HFM1	cis	parietal	SCAN
rs12567930	CCDC18	cis	parietal	SCAN
rs12567930	HFM1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91782600-91804800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:91788400-91810800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:91791200-91803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:91791400-91805400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:91793200-91819400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:91793400-91805600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:91794000-91826600	Weak transcription	Fetal Heart	heart
8	chr1:91794400-91802400	Weak transcription	Right Ventricle	heart
9	chr1:91794600-91802400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:91794800-91804600	Weak transcription	Fetal Intestine Small	intestine
11	chr1:91795000-91803800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:91795200-91802400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:91795400-91803200	Weak transcription	Brain Germinal Matrix	brain
14	chr1:91795600-91802400	Weak transcription	Fetal Lung	lung
15	chr1:91795600-91802400	Weak transcription	Ovary	ovary
16	chr1:91795600-91802400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:91795600-91802400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:91795600-91804200	Weak transcription	Pancreas	Pancrea
19	chr1:91795600-91804400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:91795600-91808000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:91795600-91824200	Weak transcription	Left Ventricle	heart
22	chr1:91795800-91802400	Weak transcription	Fetal Stomach	stomach
23	chr1:91796400-91803600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:91796600-91802400	Weak transcription	Fetal Kidney	kidney
25	chr1:91796800-91801800	Weak transcription	Fetal Brain Female	brain
26	chr1:91796800-91807800	Weak transcription	Fetal Brain Male	brain
27	chr1:91797800-91803400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:91798000-91802200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:91798800-91805800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:91799200-91804600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:91800400-91810800	Weak transcription	Brain Hippocampus Middle	brain

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