Variant report

Variant	rs12074936
Chromosome Location	chr1:10234035-10234036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10233656..10235961-chr1:10237803..10240069,2	K562	blood:

Variant related genes	Relation type
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1046277	0.82[JPT][hapmap]
rs10492970	0.82[JPT][hapmap]
rs1074461	0.83[EUR][1000 genomes]
rs11121524	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11121525	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11806008	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129751	0.83[ASN][1000 genomes]
rs17034493	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17034501	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17034569	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17034615	0.82[JPT][hapmap]
rs17034655	0.82[JPT][hapmap]
rs17034660	0.82[JPT][hapmap]
rs17034716	0.82[JPT][hapmap]
rs17034775	0.82[JPT][hapmap]
rs2273298	0.90[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2273299	0.90[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2297881	0.82[JPT][hapmap]
rs35316894	0.83[EUR][1000 genomes]
rs4846195	0.82[JPT][hapmap]
rs6667049	0.90[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs6692491	0.90[EUR][1000 genomes]
rs72864116	0.91[ASN][1000 genomes]
rs72864129	1.00[ASN][1000 genomes]
rs72864132	1.00[ASN][1000 genomes]
rs9783053	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12074936	NOL9	cis	parietal	SCAN
rs12074936	RERE	cis	parietal	SCAN
rs12074936	UBE4B	cis	parietal	SCAN
rs12074936	KIF1B	cis	parietal	SCAN
rs12074936	LZIC	cis	lymphoblastoid	seeQTL
rs12074936	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs12074936	UBE4B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10184000-10235000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:10191200-10239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:10211200-10236400	Strong transcription	Fetal Stomach	stomach
4	chr1:10213800-10236000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:10214600-10235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:10214600-10237000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:10215400-10234400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:10216200-10236400	Strong transcription	Placenta	Placenta
9	chr1:10218000-10234600	Strong transcription	Liver	Liver
10	chr1:10218200-10235800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr1:10218200-10236600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:10218400-10236200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:10221000-10236400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr1:10221000-10236600	Strong transcription	Adipose Nuclei	Adipose
15	chr1:10221800-10242200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:10222000-10236000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:10222200-10236400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:10223000-10235000	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:10223000-10237800	Weak transcription	Psoas Muscle	Psoas
20	chr1:10224400-10235000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:10224400-10235600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:10224400-10236600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:10224800-10234200	Strong transcription	Fetal Brain Female	brain
24	chr1:10224800-10236600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:10226400-10238800	Weak transcription	NHEK	skin
26	chr1:10227400-10235800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:10227600-10235400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr1:10227600-10235400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:10227600-10235400	Strong transcription	Thymus	Thymus
30	chr1:10227600-10236000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:10227600-10236400	Strong transcription	Primary B cells from cord blood	blood
32	chr1:10227600-10236400	Strong transcription	Primary T cells from cord blood	blood
33	chr1:10227600-10236400	Strong transcription	Fetal Lung	lung
34	chr1:10227600-10236600	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr1:10227600-10236600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:10227600-10236600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:10227800-10235200	Strong transcription	Brain Germinal Matrix	brain
38	chr1:10227800-10236600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:10228000-10235200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:10228000-10235400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:10228000-10235400	Strong transcription	Brain Anterior Caudate	brain
42	chr1:10228000-10235400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:10228000-10236600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:10229600-10234200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:10229600-10237800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:10230000-10234200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:10230000-10235600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:10230200-10236000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:10230200-10236400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:10230200-10237000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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