Variant report

Variant	rs2512612
Chromosome Location	chr11:67844879-67844880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:67836713..67838709-chr11:67842103..67844994,2	MCF-7	breast:
2	chr11:67842485..67845435-chr11:68038693..68040262,2	K562	blood:
3	chr11:67837349..67840620-chr11:67841779..67845406,4	K562	blood:
4	chr11:67837582..67841589-chr11:67842987..67847014,5	K562	blood:
5	chr11:67844026..67846483-chr11:67881325..67884257,2	K562	blood:
6	chr11:67810130..67812734-chr11:67842043..67845551,3	K562	blood:

Variant related genes	Relation type
ENSG00000171067	Chromatin interaction
ENSG00000110719	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10791956	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];1.00[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	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896295	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs10896298	0.81[MEX][hapmap]
rs11228129	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11228131	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11228133	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	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894204	0.80[MEX][hapmap]
rs2075609	0.84[LWK][hapmap];0.82[MKK][hapmap]
rs2457179	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457180	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[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];1.00[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];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs2511470	0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2511472	0.92[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs2511475	0.86[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2511479	0.89[JPT][hapmap]
rs2512608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2512611	1.00[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];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2512623	0.92[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3133327	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[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]
rs3935460	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]
rs4073551	1.00[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];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[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]
rs4345973	0.81[MEX][hapmap]
rs4420277	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930227	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4930557	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930561	0.81[MEX][hapmap]
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	0.82[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	0.91[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];0.85[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7931502	0.81[MEX][hapmap]
rs7940113	0.84[EUR][1000 genomes]
rs7940217	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7940501	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7944372	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs884826	0.82[CEU][hapmap]

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	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	esv2758275	chr11:67524937-67859490	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
5	nsv469856	chr11:67639037-67859490	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv482760	chr11:67639037-67859490	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
7	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
rs2512612	FGF19	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67812200-67875400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:67815000-67851400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:67819600-67846200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:67819800-67850600	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:67820000-67850800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:67821200-67845400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:67822000-67851600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:67823600-67849400	Strong transcription	Hela-S3	cervix
9	chr11:67823600-67850600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr11:67824400-67846000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:67824600-67846000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:67825200-67849600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:67825400-67845800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:67825400-67846400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:67826600-67849400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:67829800-67848600	Weak transcription	Fetal Brain Male	brain
17	chr11:67829800-67850000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:67831400-67884400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:67831600-67867000	Weak transcription	Small Intestine	intestine
20	chr11:67832600-67845000	Weak transcription	Stomach Mucosa	stomach
21	chr11:67833800-67858200	Weak transcription	HUVEC	blood vessel
22	chr11:67835400-67851200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr11:67836600-67845200	Weak transcription	Esophagus	oesophagus
24	chr11:67836600-67852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:67837600-67849200	Weak transcription	NHEK	skin
26	chr11:67838000-67845000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:67838000-67848200	Weak transcription	Aorta	Aorta
28	chr11:67838000-67867000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:67838000-67879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:67838400-67858200	Weak transcription	NH-A	brain
31	chr11:67838600-67864400	Weak transcription	Osteobl	bone
32	chr11:67838800-67852400	Weak transcription	NHDF-Ad	bronchial
33	chr11:67839000-67849200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr11:67839200-67848200	Weak transcription	Colonic Mucosa	Colon
35	chr11:67839200-67850400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:67839200-67870600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:67839400-67850000	Weak transcription	NHLF	lung
38	chr11:67839600-67847200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:67839600-67848200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:67839600-67848200	Weak transcription	HSMM	muscle
41	chr11:67839800-67849800	Weak transcription	Fetal Kidney	kidney
42	chr11:67839800-67873200	Weak transcription	Colon Smooth Muscle	Colon
43	chr11:67839800-67886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:67840800-67849400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr11:67841000-67847400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:67841400-67848200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:67841600-67845000	Weak transcription	Lung	lung
48	chr11:67841600-67848200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:67841600-67848200	Weak transcription	Thymus	Thymus
50	chr11:67841600-67850000	Weak transcription	Fetal Lung	lung

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