Variant report

Variant	rs7940501
Chromosome Location	chr11:67896560-67896561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:67895952-67896620	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr11:67896061-67896605	K562	blood:	n/a	n/a
3	CBX3	chr11:67896129-67896611	K562	blood:	n/a	n/a
4	MAX	chr11:67895082-67896736	HepG2	liver:	n/a	chr11:67896300-67896310 chr11:67896557-67896567 chr11:67895920-67895930
5	MAX	chr11:67895802-67896571	K562	blood:	n/a	chr11:67896300-67896310 chr11:67896557-67896567 chr11:67895920-67895930
6	MAZ	chr11:67895461-67896686	IMR90	lung:	n/a	chr11:67896300-67896310 chr11:67896557-67896567 chr11:67895920-67895930
7	POLR2A	chr11:67895088-67896697	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr11:67895796-67896570	K562	blood:	n/a	n/a
9	RCOR1	chr11:67896154-67896566	K562	blood:	n/a	n/a
10	POLR2A	chr11:67895223-67896675	HepG2	liver:	n/a	n/a
11	MXI1	chr11:67895799-67896915	IMR90	lung:	n/a	chr11:67896294-67896303
12	GATA1	chr11:67896037-67896663	PBDE	blood:	n/a	chr11:67896261-67896277 chr11:67896264-67896273 chr11:67896351-67896361
13	MAX	chr11:67895070-67896758	HepG2	liver:	n/a	chr11:67896300-67896310 chr11:67896557-67896567 chr11:67895920-67895930
14	MAX	chr11:67895982-67896631	H1-hESC	embryonic stem cell:	n/a	chr11:67896300-67896310 chr11:67896557-67896567
15	ZBTB7A	chr11:67895299-67896625	ECC-1	luminal epithelium:	n/a	chr11:67895540-67895548 chr11:67895682-67895690
16	HEY1	chr11:67895039-67896613	HepG2	liver:	n/a	chr11:67895901-67895916
17	YY1	chr11:67895240-67896563	HepG2	liver:	n/a	chr11:67896131-67896140 chr11:67895734-67895743 chr11:67895732-67895743 chr11:67896128-67896139
18	TBP	chr11:67895550-67896621	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZBTB7A	chr11:67895187-67896620	ECC-1	luminal epithelium:	n/a	chr11:67895540-67895548 chr11:67895682-67895690
20	NR2F2	chr11:67896069-67896563	K562	blood:	n/a	n/a
21	MYBL2	chr11:67895982-67896691	HepG2	liver:	n/a	n/a
22	UBTF	chr11:67896179-67896594	K562	blood:	n/a	n/a
23	MAZ	chr11:67895165-67896567	HepG2	liver:	n/a	chr11:67896300-67896310 chr11:67896557-67896567 chr11:67895920-67895930
24	POLR2A	chr11:67896268-67896613	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr11:67895917-67896597	H1-hESC	embryonic stem cell:	n/a	chr11:67896300-67896310 chr11:67896557-67896567 chr11:67895920-67895930
26	MAX	chr11:67895650-67896595	MCF-7	breast:	n/a	chr11:67896300-67896310 chr11:67896557-67896567 chr11:67895920-67895930
27	POLR2A	chr11:67895710-67896767	HepG2	liver:	n/a	n/a
28	MXI1	chr11:67895275-67896883	SK-N-SH	brain:	n/a	chr11:67896294-67896303

No.	Distal block	Cell Line	Cell type
1	chr11:67894406..67897015-chr11:67908475..67910662,2	K562	blood:
2	chr11:67886665..67892183-chr11:67892786..67897158,12	MCF-7	breast:
3	chr11:67895109..67896944-chr11:67898965..67901402,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCIRG1-2	chr11:67896548-67896635	XLOC_009183
2	lnc-TCIRG1-2	chr11:67896548-67896655	NONHSAT022507

Variant related genes	Relation type
ENSG00000255236	TF binding region
ENSG00000110721	Chromatin interaction
ENSG00000255236	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10791956	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10791957	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10791959	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10896293	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10896295	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896298	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs11228131	0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs11228133	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11228136	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11228137	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11228139	1.00[CEU][hapmap]
rs11228141	0.84[ASN][1000 genomes]
rs11228142	1.00[CEU][hapmap]
rs11228144	0.94[JPT][hapmap]
rs11228145	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11535788	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1894204	0.80[JPT][hapmap];0.80[MEX][hapmap]
rs2075609	0.82[LWK][hapmap];0.82[MKK][hapmap]
rs2457179	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]
rs2457180	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs2511437	0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2511467	1.00[JPT][hapmap]
rs2511468	0.83[ASN][1000 genomes]
rs2511469	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2511470	0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs2511472	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2511473	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2511475	0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2511479	1.00[JPT][hapmap]
rs2512608	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2512611	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2512612	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]
rs2512623	0.92[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2512624	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3133327	0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs3935460	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]
rs4073551	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4147780	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4345973	0.80[MEX][hapmap]
rs4420277	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4930557	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930561	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs61890478	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6591331	0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6591333	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7104982	0.91[EUR][1000 genomes]
rs7123183	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7123668	0.92[EUR][1000 genomes]
rs7124058	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71480230	0.87[EUR][1000 genomes]
rs7925022	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7925423	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7928739	0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs7931502	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs7940113	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940217	0.92[EUR][1000 genomes]
rs7944372	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884826	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs7940501	FGF19	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67889600-67897400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:67889800-67897400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:67889800-67897600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr11:67892000-67897800	Enhancers	Pancreas	Pancrea
5	chr11:67893600-67896800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr11:67894000-67898000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:67894600-67897400	Enhancers	Lung	lung
8	chr11:67895400-67896600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:67895400-67896600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr11:67895400-67896600	Active TSS	Brain Angular Gyrus	brain
11	chr11:67895400-67896600	Flanking Active TSS	Fetal Muscle Trunk	muscle
12	chr11:67895400-67896600	Flanking Active TSS	Fetal Muscle Leg	muscle
13	chr11:67895400-67896600	Enhancers	HUVEC	blood vessel
14	chr11:67895400-67897200	Enhancers	Fetal Brain Male	brain
15	chr11:67895600-67896600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:67895600-67896600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr11:67895600-67896600	Flanking Active TSS	Colonic Mucosa	Colon
18	chr11:67895600-67896600	Active TSS	Fetal Brain Female	brain
19	chr11:67895800-67896600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
20	chr11:67895800-67896600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr11:67896000-67896600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr11:67896000-67896800	Enhancers	Small Intestine	intestine
23	chr11:67896000-67896800	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr11:67896200-67896600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:67896200-67896600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:67896200-67896600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr11:67896200-67896600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr11:67896200-67896600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:67896200-67896600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr11:67896200-67896600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr11:67896200-67896600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr11:67896200-67896600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr11:67896200-67896600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:67896200-67896600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:67896200-67896600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:67896200-67896600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:67896200-67896600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr11:67896200-67896600	Flanking Active TSS	Liver	Liver
39	chr11:67896200-67896600	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr11:67896200-67896600	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr11:67896200-67896600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr11:67896200-67896600	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr11:67896200-67896600	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr11:67896200-67896600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr11:67896200-67896600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr11:67896200-67896600	Flanking Active TSS	Fetal Lung	lung
47	chr11:67896200-67896600	Bivalent Enhancer	Fetal Thymus	thymus
48	chr11:67896200-67896600	Flanking Active TSS	Psoas Muscle	Psoas
49	chr11:67896200-67896600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr11:67896200-67896600	Flanking Active TSS	Rectal Smooth Muscle	rectum

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