Variant report

Variant	rs3935460
Chromosome Location	chr11:67862084-67862085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:67854850..67857666-chr11:67861166..67863818,2	K562	blood:
2	chr11:67855551..67858335-chr11:67859728..67862327,2	K562	blood:
3	chr11:67811161..67812751-chr11:67861609..67863211,2	K562	blood:

Variant related genes	Relation type
ENSG00000110721	Chromatin interaction
ENSG00000110719	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10791956	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10791957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791959	0.83[EUR][1000 genomes]
rs10896293	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896295	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11228129	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11228131	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11228133	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11228137	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11228139	1.00[CEU][hapmap]
rs11228142	1.00[CEU][hapmap]
rs11228144	0.88[JPT][hapmap]
rs11228145	0.92[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs11535788	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11824199	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12270493	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2075609	0.86[LWK][hapmap];0.81[MKK][hapmap]
rs2457179	0.89[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457180	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511437	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511467	0.89[JPT][hapmap]
rs2511469	0.92[CEU][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs2511470	0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs2511472	0.92[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs2511475	0.85[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs2511479	0.89[JPT][hapmap]
rs2512608	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2512611	0.89[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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2512612	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2512623	0.92[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3133327	0.81[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3819255	0.92[ASN][1000 genomes]
rs4073551	0.89[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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147780	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4420277	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930227	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4930557	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61890478	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6591331	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6591333	0.90[EUR][1000 genomes]
rs7104982	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7123183	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7123668	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7124058	0.88[EUR][1000 genomes]
rs71480230	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7925022	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7925423	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7928739	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7940113	0.84[EUR][1000 genomes]
rs7940217	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7940501	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7944372	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs884826	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427892	chr11:67451649-67926562	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	esv2757450	chr11:67472905-67891289	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	112 gene(s)	inside rSNPs	diseases
3	esv2759835	chr11:67472905-67891289	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	112 gene(s)	inside rSNPs	diseases
4	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3935460	FGF19	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67812200-67875400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:67831400-67884400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:67831600-67867000	Weak transcription	Small Intestine	intestine
4	chr11:67838000-67867000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:67838000-67879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:67838600-67864400	Weak transcription	Osteobl	bone
7	chr11:67839200-67870600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:67839800-67873200	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:67839800-67886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:67842400-67867000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:67846200-67867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:67848400-67886400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:67848800-67865800	Weak transcription	K562	blood
14	chr11:67848800-67866200	Weak transcription	Right Ventricle	heart
15	chr11:67848800-67867000	Weak transcription	Placenta	Placenta
16	chr11:67848800-67874200	Weak transcription	Colonic Mucosa	Colon
17	chr11:67849000-67866400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:67849000-67866800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr11:67849000-67867000	Weak transcription	Ovary	ovary
20	chr11:67849000-67885400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr11:67849200-67867000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:67849400-67867000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:67849400-67867000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:67849400-67867000	Weak transcription	Thymus	Thymus
25	chr11:67849400-67873800	Weak transcription	Spleen	Spleen
26	chr11:67849400-67887400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:67850200-67867000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr11:67850400-67874000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:67850800-67866200	Weak transcription	Left Ventricle	heart
30	chr11:67850800-67867000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:67850800-67875200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:67851400-67864400	Weak transcription	Pancreas	Pancrea
33	chr11:67851400-67867000	Weak transcription	Psoas Muscle	Psoas
34	chr11:67851400-67873600	Weak transcription	Fetal Stomach	stomach
35	chr11:67856600-67862400	Enhancers	Brain Cingulate Gyrus	brain
36	chr11:67857400-67862200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:67857600-67862400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr11:67857600-67875000	Weak transcription	Lung	lung
39	chr11:67857800-67867200	Weak transcription	Fetal Kidney	kidney
40	chr11:67858400-67862400	Enhancers	Brain Hippocampus Middle	brain
41	chr11:67858400-67863400	Weak transcription	Gastric	stomach
42	chr11:67858600-67866200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr11:67858600-67866200	Weak transcription	Fetal Thymus	thymus
44	chr11:67858600-67866400	Weak transcription	HSMM	muscle
45	chr11:67858600-67866600	Weak transcription	HUVEC	blood vessel
46	chr11:67858600-67866800	Weak transcription	NH-A	brain
47	chr11:67858600-67867000	Weak transcription	Adipose Nuclei	Adipose
48	chr11:67858600-67867000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:67858800-67866600	Weak transcription	Primary T cells from cord blood	blood
50	chr11:67858800-67867000	Weak transcription	Primary B cells from cord blood	blood

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