Variant report

Variant	rs874269
Chromosome Location	chr19:40731945-40731946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr19:40731492-40733122	HepG2	liver:	n/a	chr19:40732929-40732939
2	CTCF	chr19:40731689-40732142	IMR90	lung:	n/a	n/a
3	SMC3	chr19:40731555-40731978	HepG2	liver:	n/a	n/a
4	SIN3AK20	chr19:40731136-40743299	PANC-1	pancreas:	n/a	n/a
5	CTCF	chr19:40731940-40732090	HPF	lung:	n/a	n/a
6	CTCF	chr19:40731820-40731970	GM12864	blood:	n/a	n/a
7	CTCF	chr19:40731880-40732030	HPAF	blood vessel:	n/a	n/a
8	CEBPB	chr19:40731775-40732130	IMR90	lung:	n/a	n/a
9	CTCF	chr19:40731800-40731950	GM12865	blood:	n/a	n/a
10	MAX	chr19:40731436-40733060	HepG2	liver:	n/a	chr19:40732929-40732939
11	CTCF	chr19:40731920-40732070	HA-sp	spinal cord:	n/a	n/a
12	CTCF	chr19:40731840-40731990	NHLF	lung:	n/a	n/a
13	RAD21	chr19:40731607-40732073	HepG2	liver:	n/a	n/a
14	STAT1	chr19:40731902-40731990	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a
16	E2F6	chr19:40731886-40733036	H1-hESC	embryonic stem cell:	n/a	chr19:40732637-40732646
17	REST	chr19:40731178-40733034	PANC-1	pancreas:	n/a	chr19:40732699-40732708 chr19:40732184-40732197
18	CEBPB	chr19:40731899-40732151	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:40731289-40733027	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40730457..40732107-chr19:40746793..40748406,2	MCF-7	breast:
2	chr19:40730620..40735723-chr19:40738673..40743679,8	MCF-7	breast:
3	chr19:40728036..40729560-chr19:40729917..40732586,2	K562	blood:
4	chr19:40730680..40732953-chr19:40742312..40745155,2	K562	blood:
5	chr19:40723230..40725206-chr19:40730553..40733160,2	MCF-7	breast:
6	chr19:40730135..40732831-chr19:40769478..40772203,2	MCF-7	breast:
7	chr19:40719578..40724896-chr19:40726262..40733162,10	MCF-7	breast:
8	chr19:40731324..40733318-chr19:40786434..40789035,2	MCF-7	breast:

No data

Variant related genes	Relation type
CNTD2	TF binding region
ENSG00000207631	Chromatin interaction
ENSG00000105221	Chromatin interaction
ENSG00000105219	Chromatin interaction
ENSG00000174521	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11666690	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11667443	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668006	0.88[CEU][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs11668520	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11669006	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669332	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670860	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670912	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11671439	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]
rs17846842	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356230	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28746190	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35090721	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs36058450	0.92[ASN][1000 genomes]
rs3730052	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730055	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730262	0.89[ASN][1000 genomes]
rs3760636	0.85[CHB][hapmap]
rs41275746	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275748	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275750	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45497695	0.80[EUR][1000 genomes]
rs56672337	0.80[EUR][1000 genomes]
rs58094119	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59058760	0.80[EUR][1000 genomes]
rs59106111	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6508937	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs66623822	0.80[EUR][1000 genomes]
rs67587726	0.80[EUR][1000 genomes]
rs7247515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252506	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73933218	0.92[ASN][1000 genomes]
rs73933225	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933232	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933236	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933237	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933238	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933240	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73933241	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs873143	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs874269	HSD17B14	cis	parietal	SCAN
rs874269	C19orf47	cis	lymphoblastoid	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40726400-40735200	Weak transcription	K562	blood
2	chr19:40729400-40732000	Weak transcription	Gastric	stomach
3	chr19:40729600-40732000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:40730600-40732000	Enhancers	Hela-S3	cervix
5	chr19:40730800-40732000	Weak transcription	Right Ventricle	heart
6	chr19:40731400-40732000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
7	chr19:40731400-40732000	Bivalent Enhancer	Fetal Intestine Small	intestine
8	chr19:40731400-40732000	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr19:40731400-40732000	Flanking Bivalent TSS/Enh	HepG2	liver
10	chr19:40731400-40732000	Bivalent Enhancer	NHEK	skin
11	chr19:40731400-40732400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
12	chr19:40731400-40732600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:40731400-40732800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr19:40731400-40732800	Enhancers	Spleen	Spleen
15	chr19:40731400-40733000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr19:40731600-40732000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
17	chr19:40731600-40732000	Bivalent Enhancer	Primary T cells from cord blood	blood
18	chr19:40731600-40732000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
19	chr19:40731600-40732000	Bivalent Enhancer	Brain Angular Gyrus	brain
20	chr19:40731600-40732000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:40731600-40732000	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr19:40731600-40732000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr19:40731600-40732000	Enhancers	Left Ventricle	heart
24	chr19:40731600-40732000	Enhancers	HSMM	muscle
25	chr19:40731600-40732000	Bivalent Enhancer	HUVEC	blood vessel
26	chr19:40731600-40732000	Flanking Active TSS	NHDF-Ad	bronchial
27	chr19:40731600-40732000	Enhancers	NHLF	lung
28	chr19:40731600-40732000	Flanking Active TSS	Osteobl	bone
29	chr19:40731600-40732200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:40731600-40732200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
31	chr19:40731600-40732200	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
32	chr19:40731600-40732400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
33	chr19:40731600-40732400	Enhancers	A549	lung
34	chr19:40731600-40732600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:40731600-40732600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:40731600-40732600	Bivalent Enhancer	Fetal Heart	heart
37	chr19:40731600-40732600	Enhancers	Placenta	Placenta
38	chr19:40731600-40732800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr19:40731600-40732800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:40731600-40732800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:40731600-40732800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:40731600-40732800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:40731600-40732800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
44	chr19:40731600-40732800	Enhancers	Lung	lung
45	chr19:40731600-40732800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
46	chr19:40731600-40732800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
47	chr19:40731600-40732800	Bivalent Enhancer	Stomach Mucosa	stomach
48	chr19:40731600-40732800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
49	chr19:40731600-40733000	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr19:40731800-40732000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell

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