Variant report

Variant	rs11671439
Chromosome Location	chr19:40778177-40778178
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	MAX	chr19:40778048-40778531	K562	blood:	n/a	chr19:40778286-40778295 chr19:40778287-40778294
2	POLR2A	chr19:40778074-40778473	K562	blood:	n/a	n/a
3	MYC	chr19:40778104-40779038	K562	blood:	n/a	chr19:40778286-40778295 chr19:40778287-40778294
4	POLR2A	chr19:40778150-40778659	SK-N-MC	brain:	n/a	n/a
5	TEAD4	chr19:40778088-40779191	K562	blood:	n/a	n/a
6	POLR2A	chr19:40778078-40779164	K562	blood:	n/a	n/a
7	MAX	chr19:40778153-40778578	K562	blood:	n/a	chr19:40778286-40778295 chr19:40778287-40778294
8	POLR2A	chr19:40777778-40778598	GM12878	blood:	n/a	n/a
9	CUX1	chr19:40778154-40779040	K562	blood:	n/a	n/a
10	POLR2A	chr19:40777969-40778651	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40776468..40779839-chr19:40784717..40787633,5	MCF-7	breast:
2	chr19:40769216..40771181-chr19:40778063..40779733,2	K562	blood:
3	chr19:40776878..40778500-chr19:40970454..40972142,2	K562	blood:

Variant related genes	Relation type
AKT2	TF binding region
ENSG00000105221	Chromatin interaction
ENSG00000090013	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11665880	0.83[EUR][1000 genomes]
rs11666690	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666860	0.82[EUR][1000 genomes]
rs11667443	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667768	0.84[EUR][1000 genomes]
rs11667774	0.84[EUR][1000 genomes]
rs11668006	0.88[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11668520	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11669006	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669332	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670323	0.87[EUR][1000 genomes]
rs11670860	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670912	0.86[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17846842	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356230	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28746190	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35090721	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36058450	0.84[ASN][1000 genomes]
rs3730052	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3730055	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3730259	0.85[CHB][hapmap]
rs3730262	0.82[ASN][1000 genomes]
rs41275746	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41275748	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41275750	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45497695	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56672337	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58094119	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59058760	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59106111	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6508937	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66623822	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67587726	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7245751	0.87[EUR][1000 genomes]
rs7247515	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7249819	0.84[EUR][1000 genomes]
rs7252506	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73933218	0.84[ASN][1000 genomes]
rs73933225	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933232	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933236	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933237	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933238	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933240	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933241	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105478	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs873143	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874269	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1064502	chr19:40758049-40781360	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1063993	chr19:40763787-40781360	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1059884	chr19:40763839-40781360	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1057052	chr19:40776128-40789766	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11671439	HSD17B14	cis	parietal	SCAN
rs11671439	C19orf47	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40759800-40780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:40762000-40779800	Weak transcription	Stomach Mucosa	stomach
3	chr19:40762800-40780800	Weak transcription	Small Intestine	intestine
4	chr19:40766200-40788600	Weak transcription	HSMMtube	muscle
5	chr19:40767600-40779600	Strong transcription	Fetal Stomach	stomach
6	chr19:40767800-40780400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:40768200-40780400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:40769000-40778200	Weak transcription	HSMM	muscle
9	chr19:40769000-40779600	Strong transcription	Fetal Intestine Small	intestine
10	chr19:40769600-40783600	Weak transcription	Fetal Kidney	kidney
11	chr19:40770000-40789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:40770000-40789600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:40770200-40789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
15	chr19:40770400-40784000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:40771000-40780400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:40771000-40780800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr19:40771000-40783600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:40771400-40778200	Enhancers	Left Ventricle	heart
20	chr19:40771400-40779400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:40771400-40789400	Weak transcription	HUVEC	blood vessel
22	chr19:40771600-40780400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr19:40771600-40786000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:40772000-40778200	Weak transcription	Dnd41	blood
25	chr19:40773600-40779600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:40773800-40780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:40774200-40778200	Weak transcription	Colonic Mucosa	Colon
28	chr19:40774400-40778400	Strong transcription	NHEK	skin
29	chr19:40774400-40778800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr19:40774600-40778200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:40774600-40778200	Weak transcription	Placenta	Placenta
32	chr19:40774600-40778400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:40774600-40780000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:40774600-40780000	Weak transcription	NHDF-Ad	bronchial
35	chr19:40774800-40779600	Weak transcription	Colon Smooth Muscle	Colon
36	chr19:40774800-40780400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr19:40775400-40778200	Enhancers	Brain Angular Gyrus	brain
38	chr19:40775600-40778600	Weak transcription	HepG2	liver
39	chr19:40775800-40778400	Genic enhancers	Fetal Muscle Leg	muscle
40	chr19:40776000-40779800	Weak transcription	Brain Germinal Matrix	brain
41	chr19:40776000-40787400	Weak transcription	A549	lung
42	chr19:40776200-40778200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr19:40776200-40778800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:40776200-40780400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:40776400-40778400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:40776400-40778600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr19:40776400-40779400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr19:40776400-40779800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:40776400-40780400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr19:40776400-40785000	Weak transcription	NHLF	lung

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