Variant report

Variant	rs7959497
Chromosome Location	chr12:49592117-49592118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49581166..49587086-chr12:49589804..49595729,8	K562	blood:
2	chr12:49591818..49595600-chr12:49658262..49660804,4	K562	blood:
3	chr12:49554137..49556960-chr12:49591128..49592792,2	K562	blood:
4	chr12:49522795..49526173-chr12:49587033..49593162,7	K562	blood:

Variant related genes	Relation type
ENSG00000167552	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1039225	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap]
rs10747561	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs10747562	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs10747563	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10783302	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs10783308	0.83[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap]
rs10875924	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs10875928	0.83[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap]
rs10875931	0.83[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.80[ASN][1000 genomes]
rs10875934	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875935	0.84[CHB][hapmap]
rs11168857	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap]
rs11168862	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs11168884	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs11168893	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs11168904	0.80[ASN][1000 genomes]
rs11168910	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap]
rs11168911	0.95[ASN][1000 genomes]
rs11168912	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168917	0.95[ASN][1000 genomes]
rs11168919	0.95[ASN][1000 genomes]
rs12229524	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap]
rs12309994	0.95[ASN][1000 genomes]
rs1476137	0.83[CEU][hapmap]
rs1874908	0.83[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap]
rs1991427	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs2047101	0.87[CEU][hapmap];0.94[CHB][hapmap]
rs2162644	0.94[CHB][hapmap]
rs2279596	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap]
rs2334930	0.83[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs2334931	0.80[ASN][1000 genomes]
rs2753	0.83[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap]
rs3741621	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap]
rs56149019	0.95[ASN][1000 genomes]
rs7306084	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs731350	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs7953169	0.80[ASN][1000 genomes]
rs7954521	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs7954530	0.83[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.80[ASN][1000 genomes]
rs7957998	0.87[CEU][hapmap];0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs7958241	0.88[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap]
rs7969967	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap]
rs7978448	0.87[CEU][hapmap]
rs9325145	0.83[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7959497	RHEBL1	cis	parietal	SCAN
rs7959497	OR10AD1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49583000-49592200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:49583200-49595800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:49583400-49595800	Weak transcription	Ovary	ovary
4	chr12:49583600-49592200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:49583600-49592400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:49583600-49592400	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:49583600-49594600	Weak transcription	Fetal Kidney	kidney
8	chr12:49583600-49595800	Weak transcription	Aorta	Aorta
9	chr12:49583600-49595800	Weak transcription	Fetal Thymus	thymus
10	chr12:49583800-49592400	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:49583800-49592400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:49584000-49592200	Weak transcription	NHLF	lung
13	chr12:49584200-49594200	Weak transcription	A549	lung
14	chr12:49584400-49592400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:49584600-49592400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:49584600-49592400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:49585200-49592200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:49585200-49592200	Weak transcription	Fetal Brain Male	brain
19	chr12:49590000-49592200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:49591000-49592200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr12:49591000-49592200	Enhancers	Brain Germinal Matrix	brain
22	chr12:49591000-49596200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:49591200-49592200	Enhancers	Brain Anterior Caudate	brain
24	chr12:49591200-49592200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr12:49591200-49592400	Enhancers	Brain Hippocampus Middle	brain
26	chr12:49591200-49592400	Enhancers	HUVEC	blood vessel
27	chr12:49591200-49592600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:49591200-49593200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:49591200-49593400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:49591400-49592400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:49591400-49592400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:49591400-49592600	Enhancers	Brain Substantia Nigra	brain
33	chr12:49591600-49592600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:49591600-49594000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:49591600-49594200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:49591600-49594400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr12:49591600-49594600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:49591600-49594600	Weak transcription	Adipose Nuclei	Adipose
39	chr12:49591600-49594600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr12:49591600-49594800	Weak transcription	Primary B cells from cord blood	blood
41	chr12:49591600-49595800	Weak transcription	Spleen	Spleen
42	chr12:49591800-49592200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:49591800-49592400	Enhancers	Osteobl	bone
44	chr12:49591800-49592600	Enhancers	Brain Angular Gyrus	brain
45	chr12:49591800-49594200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:49592000-49592400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:49592000-49592400	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr12:49592000-49592400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:49592000-49592400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:49592000-49592400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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