Variant report

Variant	rs3124814
Chromosome Location	chr1:186339878-186339879
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:186294851..186296837-chr1:186338357..186340911,2	K562	blood:
2	chr1:186318410..186320911-chr1:186337903..186340668,2	K562	blood:
3	chr1:186307526..186309096-chr1:186339820..186342574,2	K562	blood:

Variant related genes	Relation type
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10494586	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911855	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16825295	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1919198	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2026187	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037830	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141393	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2178215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2383476	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3115761	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131550	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3131551	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131558	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3766706	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766708	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766709	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[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];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425026	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657726	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700930	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7756	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878041	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8824	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1847807	chr1:186295930-186339878	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv548399	chr1:186295930-186353461	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
5	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3124814	C1orf27	cis	cerebellum	SCAN
rs3124814	OCLM	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186277600-186342600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:186278400-186342600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:186279400-186342400	Strong transcription	Fetal Thymus	thymus
4	chr1:186279600-186342400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:186280000-186340400	Strong transcription	Dnd41	blood
6	chr1:186280000-186342000	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:186280000-186342400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:186280000-186342400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:186280000-186342400	Strong transcription	Osteobl	bone
10	chr1:186280000-186342600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:186280000-186342600	Strong transcription	HSMM	muscle
12	chr1:186280200-186342200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:186280400-186342400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr1:186280800-186342600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:186281000-186341800	Strong transcription	Liver	Liver
16	chr1:186281000-186342600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:186281200-186341400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr1:186281200-186341800	Strong transcription	Adipose Nuclei	Adipose
19	chr1:186281200-186342200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:186281200-186342200	Strong transcription	NH-A	brain
21	chr1:186281400-186341600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:186281400-186342000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:186281400-186342000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:186281400-186342000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:186281400-186342200	Strong transcription	Hela-S3	cervix
26	chr1:186281400-186342400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:186281400-186342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:186281800-186342200	Strong transcription	K562	blood
29	chr1:186283400-186341000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:186285200-186342200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:186287000-186343400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:186290000-186342000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:186293200-186340000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:186293800-186340400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:186294400-186341000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:186296600-186341400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:186298200-186341400	Strong transcription	Primary B cells from cord blood	blood
38	chr1:186298200-186341400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:186298200-186341600	Strong transcription	A549	lung
40	chr1:186299200-186342000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:186307400-186342000	Strong transcription	Fetal Intestine Large	intestine
42	chr1:186312200-186341600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:186318000-186342200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:186318400-186342200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:186318600-186342200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:186318600-186342200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:186318600-186342600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:186318800-186342000	Strong transcription	HUVEC	blood vessel
49	chr1:186320200-186342000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:186320800-186342200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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