Variant report

Variant	rs12037177
Chromosome Location	chr1:155877029-155877030
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	chr1:155868953..155871356-chr1:155876102..155879060,2	MCF-7	breast:
2	chr1:155874036..155877922-chr1:155878278..155881350,6	K562	blood:

Variant related genes	Relation type
ENSG00000143622	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10796955	0.95[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs10908483	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1111102	0.81[CEU][hapmap]
rs11264426	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs11585845	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs12026057	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080846	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12091273	0.87[AFR][1000 genomes]
rs12091361	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12118795	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs12144175	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12568523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs1889532	0.95[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs1889533	0.82[AMR][1000 genomes]
rs2016251	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2282301	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297649	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2364403	0.92[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3820594	0.81[MEX][hapmap]
rs4661218	0.95[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs6427297	0.81[TSI][hapmap]
rs66466805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66669006	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6667652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6670477	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6670493	0.95[CEU][hapmap]
rs6696019	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72708205	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7528441	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7534858	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs7545308	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs867548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs867549	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs867550	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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs915178	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs915181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs928596	0.95[CEU][hapmap];0.86[MEX][hapmap];0.85[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	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12037177	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs12037177	HAPLN2	cis	parietal	SCAN
rs12037177	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12037177	YY1AP1	cis	cerebellum	SCAN
rs12037177	RIT1	cis	Thyroid	GTEx
rs12037177	ROBLD3	cis	parietal	SCAN
rs12037177	RIT1	cis	cerebellum	SCAN
rs12037177	RIT1	cis	multi-tissue	Pritchard
rs12037177	SPRR3	cis	parietal	SCAN
rs12037177	PRUNE	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155863400-155880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155865200-155878600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:155865200-155879200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:155865200-155879600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:155865600-155879200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:155865600-155879600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:155865800-155878400	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr1:155865800-155878800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:155865800-155879200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:155865800-155879400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:155865800-155879800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155865800-155880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:155866000-155879000	Strong transcription	Liver	Liver
14	chr1:155866000-155879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:155866000-155879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:155866000-155879200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:155866000-155879600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:155866000-155879600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:155866000-155879600	Strong transcription	Fetal Intestine Large	intestine
20	chr1:155866000-155879800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:155866000-155879800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:155866000-155879800	Strong transcription	Fetal Thymus	thymus
23	chr1:155866200-155879000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:155866200-155879000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:155866200-155879800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:155866400-155877600	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:155866400-155878000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:155866400-155879200	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:155866400-155879600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:155866400-155879800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:155866600-155878400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:155866800-155879000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:155867400-155878600	Strong transcription	Dnd41	blood
34	chr1:155867400-155879800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:155867400-155879800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:155867400-155880000	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:155868400-155877600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr1:155868400-155879400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:155868600-155879200	Strong transcription	Adipose Nuclei	Adipose
40	chr1:155868600-155879400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr1:155868800-155877400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:155868800-155878800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:155868800-155879400	Strong transcription	Left Ventricle	heart
44	chr1:155868800-155879800	Strong transcription	Thymus	Thymus
45	chr1:155868800-155880000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:155869000-155877400	Strong transcription	Pancreas	Pancrea
47	chr1:155869000-155877400	Strong transcription	HSMMtube	muscle
48	chr1:155869000-155879000	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr1:155869000-155879800	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:155869000-155879800	Strong transcription	Fetal Stomach	stomach

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