Variant report

Variant	rs3115761
Chromosome Location	chr1:186347693-186347694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10494586	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911855	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16825295	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1919198	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2026187	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2141393	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178215	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2383476	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3124814	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	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3131551	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766708	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3766709	1.00[ASW][hapmap];0.96[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];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425026	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657726	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700930	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7756	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs878041	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]
rs8824	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	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
rs3115761	C1orf27	cis	cerebellum	SCAN
rs3115761	OCLM	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186342800-186349000	Active TSS	GM12878-XiMat	blood
2	chr1:186345400-186358000	Weak transcription	Left Ventricle	heart
3	chr1:186345400-186358600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:186345400-186359000	Weak transcription	Lung	lung
5	chr1:186345400-186371600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:186345400-186371600	Weak transcription	Esophagus	oesophagus
7	chr1:186345400-186371600	Weak transcription	Gastric	stomach
8	chr1:186345400-186390600	Weak transcription	Small Intestine	intestine
9	chr1:186345400-186398200	Weak transcription	Spleen	Spleen
10	chr1:186345800-186349800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:186345800-186361200	Weak transcription	Aorta	Aorta
12	chr1:186345800-186377400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:186346000-186349200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:186346000-186353200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:186346000-186366800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:186346200-186347800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:186346200-186348200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:186346200-186348600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:186346200-186348600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:186346200-186348600	Weak transcription	Placenta	Placenta
21	chr1:186346200-186348600	Weak transcription	Fetal Thymus	thymus
22	chr1:186346200-186348800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:186346200-186349000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:186346200-186349000	Weak transcription	Fetal Intestine Large	intestine
25	chr1:186346200-186349200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:186346200-186349200	Weak transcription	Primary B cells from cord blood	blood
27	chr1:186346200-186349200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:186346200-186349400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:186346200-186349600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:186346200-186349600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:186346200-186349600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:186346200-186349600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:186346200-186349600	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:186346200-186350400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:186346200-186350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:186346200-186350600	Weak transcription	Fetal Stomach	stomach
37	chr1:186346200-186350800	Weak transcription	HSMMtube	muscle
38	chr1:186346200-186351400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:186346200-186351800	Weak transcription	Fetal Lung	lung
40	chr1:186346200-186357400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:186346200-186357800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:186346200-186357800	Weak transcription	Brain Anterior Caudate	brain
43	chr1:186346200-186357800	Weak transcription	Fetal Kidney	kidney
44	chr1:186346200-186359000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:186346200-186359000	Weak transcription	Ovary	ovary
46	chr1:186346200-186359000	Weak transcription	Thymus	Thymus
47	chr1:186346200-186360600	Weak transcription	Brain Substantia Nigra	brain
48	chr1:186346200-186361200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:186346200-186361200	Weak transcription	Pancreas	Pancrea
50	chr1:186346200-186361400	Weak transcription	Right Ventricle	heart

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