Variant report

Variant	rs2384992
Chromosome Location	chr19:18386798-18386799
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18382150-18392613	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:18385060-18387078	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:18384624-18387036	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:18385122-18388006	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:18384529-18386988	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr19:18386266-18386884	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr19:18385294-18386851	U87	brain:	n/a	n/a
8	POLR2A	chr19:18385002-18394564	K562	blood:	n/a	n/a
9	POLR2A	chr19:18384933-18386934	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:18385060-18387122	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:18382160-18394577	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:18385094-18386861	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:18385003-18386852	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:18386222-18386832	U87	brain:	n/a	n/a
15	POLR2A	chr19:18385064-18387080	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:18382204-18393752	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr19:18384125-18394577	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr19:18384987-18386940	HL-60	blood:	n/a	n/a
19	POLR2A	chr19:18384132-18387127	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:18384885-18386907	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:18386327-18386846	K562	blood:	n/a	n/a
22	POLR2A	chr19:18382072-18393931	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr19:18384046-18388039	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:18384929-18387402	GM12891	blood:	n/a	n/a
25	POLR2A	chr19:18385533-18386926	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:18386759-18386811	ProgFib	skin:	n/a	n/a
27	POLR2A	chr19:18384931-18387011	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:18384198-18387461	GM12892	blood:	n/a	n/a
29	POLR2A	chr19:18385134-18387368	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr19:18384753-18387294	GM12891	blood:	n/a	n/a
31	POLR2A	chr19:18384283-18387480	GM12891	blood:	n/a	n/a
32	POLR2A	chr19:18384226-18387464	K562	blood:	n/a	n/a
33	POLR2A	chr19:18384333-18387883	A549	lung:	n/a	n/a
34	POLR2A	chr19:18385105-18387460	K562	blood:	n/a	n/a
35	POLR2A	chr19:18385428-18386845	K562	blood:	n/a	n/a
36	POLR2A	chr19:18385202-18386857	U87	brain:	n/a	n/a
37	POLR2A	chr19:18386131-18386993	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:18385181-18386832	U87	brain:	n/a	n/a
39	POLR2A	chr19:18384132-18387930	GM12891	blood:	n/a	n/a
40	POLR2A	chr19:18386225-18386837	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr19:18384368-18387934	HepG2	liver:	n/a	n/a
42	POLR2A	chr19:18384522-18387457	K562	blood:	n/a	n/a
43	POLR2A	chr19:18385004-18393940	PBDE	blood:	n/a	n/a
44	POLR2A	chr19:18379986-18394443	IMR90	lung:	n/a	n/a
45	POLR2A	chr19:18384124-18388692	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:18385071-18386829	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr19:18384541-18393878	K562	blood:	n/a	n/a
48	POLR2A	chr19:18385116-18387456	K562	blood:	n/a	n/a
49	POLR2A	chr19:18384992-18387052	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr19:18384984-18386840	HCT-116	colon:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18385043..18394940-chr19:18518893..18533267,53	K562	blood:
2	chr19:18303093..18307365-chr19:18386584..18393500,10	K562	blood:
3	chr19:18313659..18316582-chr19:18386529..18393683,9	K562	blood:
4	chr19:18260692..18269532-chr19:18383927..18395911,19	K562	blood:
5	chr19:18266311..18268091-chr19:18385667..18387246,2	K562	blood:
6	chr19:18384108..18395354-chr19:18534355..18544725,18	K562	blood:
7	chr19:18382564..18395263-chr19:18409643..18446343,165	MCF-7	breast:
8	chr19:18302787..18307396-chr19:18383842..18390051,8	K562	blood:
9	chr19:18385174..18387255-chr19:18528960..18531893,2	MCF-7	breast:
10	chr19:18337494..18340607-chr19:18385389..18388339,3	K562	blood:
11	chr19:18385251..18388025-chr19:18541664..18544540,2	K562	blood:
12	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:
13	chr19:18386246..18388460-chr6:43139240..43141141,2	K562	blood:
14	chr19:18367098..18369243-chr19:18385751..18387528,2	MCF-7	breast:
15	chr19:18385704..18387487-chr19:18538825..18541635,2	K562	blood:
16	chr19:18076357..18078652-chr19:18385740..18388342,2	K562	blood:
17	chr19:18364898..18366425-chr19:18385425..18387371,2	MCF-7	breast:

No data

Variant related genes	Relation type
KIAA1683	TF binding region
ENSG00000105647	Chromatin interaction
ENSG00000221167	Chromatin interaction
ENSG00000239821	Chromatin interaction
ENSG00000105649	Chromatin interaction
ENSG00000269145	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000105650	Chromatin interaction
ENSG00000130520	Chromatin interaction
ENSG00000254858	Chromatin interaction
ENSG00000105642	Chromatin interaction
ENSG00000112658	Chromatin interaction
ENSG00000268650	Chromatin interaction
ENSG00000268173	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12462798	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609001	0.86[CHD][hapmap]
rs12979985	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1549142	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17797780	0.84[CHD][hapmap]
rs2277921	0.81[CHD][hapmap]
rs2384991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384993	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41519246	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4254438	0.87[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4378729	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55766362	0.84[ASN][1000 genomes]
rs67482294	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7249	0.81[ASN][1000 genomes]
rs7252586	0.82[ASN][1000 genomes]
rs8103177	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
6	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
7	nsv911260	chr19:18288069-18386798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv470131	chr19:18326222-18389135	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
10	nsv911267	chr19:18351674-18386798	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv911268	chr19:18351674-18395537	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
12	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
13	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
14	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
15	nsv828472	chr19:18377725-18404131	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
16	esv1833305	chr19:18378219-18408222	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
17	nsv911272	chr19:18378219-18439383	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
18	nsv578744	chr19:18380072-18392873	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
19	esv1793726	chr19:18381600-18400786	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	104 gene(s)	inside rSNPs	diseases
20	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2384992	FLJ25328	cis	parietal	SCAN
rs2384992	KIAA1683	cis	cerebellum	SCAN
rs2384992	OR10H5	cis	cerebellum	SCAN
rs2384992	ZNF429	cis	parietal	SCAN
rs2384992	PLVAP	cis	parietal	SCAN
rs2384992	ISYNA1	cis	cerebellum	SCAN
rs2384992	MRPL34	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18366400-18389400	Weak transcription	Fetal Brain Male	brain
2	chr19:18366600-18390000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:18374600-18388400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:18375000-18388200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:18377200-18388800	Weak transcription	Dnd41	blood
6	chr19:18377800-18388800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:18378200-18388800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:18378200-18389000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:18379400-18387600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:18379400-18388800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:18379400-18388800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:18379400-18389000	Weak transcription	Aorta	Aorta
13	chr19:18380400-18388800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:18380400-18388800	Weak transcription	Fetal Brain Female	brain
15	chr19:18383800-18387800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:18384000-18388800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr19:18384200-18387200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:18384200-18387200	Genic enhancers	Fetal Intestine Small	intestine
19	chr19:18384200-18387200	Enhancers	Pancreas	Pancrea
20	chr19:18384400-18386800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:18384400-18387000	Enhancers	Esophagus	oesophagus
22	chr19:18384400-18387200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr19:18384400-18387400	Genic enhancers	Fetal Muscle Leg	muscle
24	chr19:18384400-18388200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr19:18384400-18388800	Genic enhancers	Placenta	Placenta
26	chr19:18384400-18389000	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr19:18384600-18386800	Enhancers	Right Ventricle	heart
28	chr19:18384600-18387000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:18384600-18387000	Enhancers	Psoas Muscle	Psoas
30	chr19:18384600-18387000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr19:18384600-18387000	Enhancers	HMEC	breast
32	chr19:18384600-18387600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:18384600-18388800	Strong transcription	Thymus	Thymus
34	chr19:18384600-18389000	Genic enhancers	Fetal Intestine Large	intestine
35	chr19:18384600-18389800	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr19:18385000-18386800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:18385000-18386800	Enhancers	Brain Anterior Caudate	brain
38	chr19:18385000-18386800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:18385000-18386800	Enhancers	Left Ventricle	heart
40	chr19:18385000-18386800	Enhancers	NH-A	brain
41	chr19:18385000-18387000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:18385000-18387000	Enhancers	Ovary	ovary
43	chr19:18385000-18388800	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr19:18385200-18386800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:18385200-18386800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr19:18385200-18386800	Enhancers	Brain Cingulate Gyrus	brain
47	chr19:18385200-18386800	Enhancers	Right Atrium	heart
48	chr19:18385200-18386800	Flanking Active TSS	Hela-S3	cervix
49	chr19:18385200-18386800	Enhancers	HSMM	muscle
50	chr19:18385200-18386800	Enhancers	HUVEC	blood vessel

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