Variant report

Variant	rs12760267
Chromosome Location	chr1:91869489-91869490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:91850497..91852225-chr1:91868597..91870253,2	K562	blood:
2	chr1:91867702..91872217-chr1:91965179..91968319,5	K562	blood:
3	chr1:91747960..91748866-chr1:91869014..91869895,2	MCF-7	breast:
4	chr1:91858513..91860821-chr1:91867811..91869915,2	K562	blood:

Variant related genes	Relation type
ENSG00000097046	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12567679	0.84[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs12567930	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]
rs12729858	0.91[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12756869	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12759453	0.84[AMR][1000 genomes]
rs17131418	0.91[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1974253	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2060997	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2099749	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35081855	0.81[AMR][1000 genomes]
rs35462750	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs920469	0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12760267	CCDC18	cis	parietal	SCAN
rs12760267	HFM1	cis	parietal	SCAN
rs12760267	ABCA4	cis	parietal	SCAN
rs12760267	HFM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91853200-91869600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:91863600-91869600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:91864200-91869600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:91865000-91869600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:91866200-91869600	Weak transcription	Psoas Muscle	Psoas
6	chr1:91867000-91869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:91867200-91869600	Weak transcription	Adipose Nuclei	Adipose
8	chr1:91868000-91869600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:91868800-91870600	Active TSS	K562	blood
10	chr1:91868800-91870800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:91868800-91871000	Weak transcription	Fetal Heart	heart
12	chr1:91869000-91870800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:91869000-91871000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:91869200-91870600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:91869200-91870600	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:91869200-91870600	Active TSS	Brain Germinal Matrix	brain
17	chr1:91869200-91870800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:91869200-91870800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:91869200-91870800	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:91869200-91871000	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr1:91869400-91869600	Enhancers	Primary B cells from peripheral blood	blood
22	chr1:91869400-91869600	Active TSS	Primary hematopoietic stem cells	blood
23	chr1:91869400-91869600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:91869400-91869600	Active TSS	Fetal Intestine Small	intestine
25	chr1:91869400-91869600	Active TSS	Fetal Muscle Leg	muscle
26	chr1:91869400-91869600	Bivalent/Poised TSS	HUVEC	blood vessel
27	chr1:91869400-91869800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:91869400-91869800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:91869400-91869800	Active TSS	Fetal Intestine Large	intestine
30	chr1:91869400-91870000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:91869400-91870400	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr1:91869400-91870600	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr1:91869400-91870600	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr1:91869400-91870600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:91869400-91870600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:91869400-91870600	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:91869400-91870600	Active TSS	Fetal Kidney	kidney
38	chr1:91869400-91870600	Active TSS	Fetal Lung	lung
39	chr1:91869400-91870600	Active TSS	Fetal Stomach	stomach
40	chr1:91869400-91870800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr1:91869400-91870800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:91869400-91870800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:91869400-91870800	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr1:91869400-91870800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:91869400-91870800	Active TSS	Brain Anterior Caudate	brain
46	chr1:91869400-91870800	Active TSS	Fetal Brain Female	brain
47	chr1:91869400-91870800	Active TSS	Ovary	ovary
48	chr1:91869400-91870800	Active TSS	Stomach Smooth Muscle	stomach
49	chr1:91869400-91870800	Active TSS	NH-A	brain
50	chr1:91869400-91871000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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