Variant report

Variant	rs878041
Chromosome Location	chr1:186329257-186329258
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:186291622..186294761-chr1:186327186..186330019,3	K562	blood:
2	chr1:186321243..186327284-chr1:186327473..186331831,10	K562	blood:
3	chr1:186288812..186291873-chr1:186327325..186329603,3	MCF-7	breast:
4	chr1:186292652..186294761-chr1:186327186..186329585,2	K562	blood:

Variant related genes	Relation type
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10494586	1.00[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16825295	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1919198	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2026187	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037830	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178215	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2383476	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3115761	0.83[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3124814	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]
rs3131550	0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3131551	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3131558	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3766706	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766708	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3766709	0.83[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6425026	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6657726	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6700930	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs7756	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8824	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs878041	C1orf27	cis	cerebellum	SCAN
rs878041	OCLM	cis	cerebellum	SCAN
rs878041	OCLM	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr1:186281200-186338200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr1:186281200-186341400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:186281200-186341800	Strong transcription	Adipose Nuclei	Adipose
20	chr1:186281200-186342200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:186281200-186342200	Strong transcription	NH-A	brain
22	chr1:186281400-186341600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:186281400-186342000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:186281400-186342000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:186281400-186342000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:186281400-186342200	Strong transcription	Hela-S3	cervix
27	chr1:186281400-186342400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:186281400-186342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:186281800-186335600	Strong transcription	HMEC	breast
30	chr1:186281800-186342200	Strong transcription	K562	blood
31	chr1:186283400-186341000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:186285200-186342200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:186287000-186343400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:186290000-186342000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr1:186293200-186340000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:186293800-186340400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:186294400-186341000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:186294800-186338800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:186296600-186341400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:186298200-186338200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:186298200-186341400	Strong transcription	Primary B cells from cord blood	blood
42	chr1:186298200-186341400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:186298200-186341600	Strong transcription	A549	lung
44	chr1:186298600-186337200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr1:186298600-186338600	Strong transcription	Primary T cells from cord blood	blood
46	chr1:186299200-186342000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:186299400-186338600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:186299600-186331200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:186307400-186342000	Strong transcription	Fetal Intestine Large	intestine
50	chr1:186307600-186331800	Strong transcription	Placenta Amnion	Placenta Amnion

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