Variant report

Variant	rs655717
Chromosome Location	chr11:73684215-73684216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:73683126-73685543	K562	blood:	n/a	n/a
2	POLR2A	chr11:73683045-73687212	GM12892	blood:	n/a	n/a
3	POLR2A	chr11:73683064-73684852	K562	blood:	n/a	n/a
4	POLR2A	chr11:73683106-73684644	GM12891	blood:	n/a	n/a
5	POLR2A	chr11:73683064-73685810	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:73683089-73684708	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:73683171-73684745	K562	blood:	n/a	n/a
8	POLR2A	chr11:73683181-73684767	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:73683712-73684527	A549	lung:	n/a	n/a
10	POLR2A	chr11:73683176-73684371	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr11:73679479-73686782	K562	blood:	n/a	n/a
12	POLR2A	chr11:73684182-73684663	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:73683196-73684789	GM18951	blood:	n/a	n/a
14	POLR2A	chr11:73680396-73687250	GM12892	blood:	n/a	n/a
15	MTA3	chr11:73683042-73684552	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:73683130-73684694	GM19099	blood:	n/a	n/a
17	TEAD4	chr11:73683670-73684316	K562	blood:	n/a	n/a
18	ZNF143	chr11:73684173-73684369	K562	blood:	n/a	n/a
19	POLR2A	chr11:73683786-73684302	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:73678522-73695046	PBDE	blood:	n/a	n/a
21	POLR2A	chr11:73683218-73684698	K562	blood:	n/a	n/a
22	POLR2A	chr11:73682016-73686824	GM12892	blood:	n/a	n/a
23	POLR2A	chr11:73679749-73686894	GM12891	blood:	n/a	n/a
24	POLR2A	chr11:73682119-73684741	GM18526	blood:	n/a	n/a
25	POLR2A	chr11:73683153-73684789	GM12878	blood:	n/a	n/a
26	POLR2A	chr11:73680627-73684733	Raji	blood:	n/a	n/a
27	POLR2A	chr11:73681127-73686994	K562	blood:	n/a	n/a
28	POLR2A	chr11:73679760-73685825	GM12878	blood:	n/a	n/a
29	POLR2A	chr11:73679570-73684863	K562	blood:	n/a	n/a
30	POLR2A	chr11:73684186-73684402	A549	lung:	n/a	n/a
31	POLR2A	chr11:73684177-73684409	A549	lung:	n/a	n/a
32	POLR2A	chr11:73682146-73684701	K562	blood:	n/a	n/a
33	STAT5A	chr11:73683063-73684334	GM12878	blood:	n/a	n/a
34	NFATC1	chr11:73683045-73684257	GM12878	blood:	n/a	n/a
35	POLR2A	chr11:73683139-73684734	GM15510	blood:	n/a	n/a
36	POLR2A	chr11:73680903-73685494	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr11:73683172-73684731	K562	blood:	n/a	n/a
38	POLR2A	chr11:73683090-73684825	K562	blood:	n/a	n/a
39	POLR2A	chr11:73679439-73686847	GM18505	blood:	n/a	n/a
40	POLR2A	chr11:73683077-73684805	HL-60	blood:	n/a	n/a
41	POLR2A	chr11:73683035-73687243	GM12878	blood:	n/a	n/a
42	PML	chr11:73683029-73684770	GM12878	blood:	n/a	n/a
43	POLR2A	chr11:73683209-73684815	NB4	blood:	n/a	n/a
44	POLR2A	chr11:73683143-73684775	K562	blood:	n/a	n/a
45	PML	chr11:73683102-73684818	K562	blood:	n/a	n/a
46	POLR2A	chr11:73682064-73684796	GM12878	blood:	n/a	n/a
47	POLR2A	chr11:73682871-73685271	HepG2	liver:	n/a	n/a
48	POLR2A	chr11:73683064-73684743	GM12891	blood:	n/a	n/a
49	NFATC1	chr11:73683059-73684372	GM12878	blood:	n/a	n/a
50	POLR2A	chr11:73683057-73684810	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:73681646..73684288-chr11:73745260..73748147,2	MCF-7	breast:
2	chr11:73679561..73684546-chr11:73778723..73783416,5	MCF-7	breast:
3	chr1:6295909..6296442-chr11:73684076..73684675,2	NB4	blood:

No data

Variant related genes	Relation type
ENSG00000255847	TF binding region
ENSG00000116237	Chromatin interaction
ENSG00000168014	Chromatin interaction
ENSG00000225077	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1685355	0.86[CHB][hapmap]
rs1726745	0.82[CHB][hapmap]
rs3019463	0.88[ASN][1000 genomes]
rs34408426	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs586773	0.88[ASN][1000 genomes]
rs588097	0.82[CHB][hapmap]
rs591758	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs599277	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603950	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs605442	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs621976	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs632862	0.88[ASN][1000 genomes]
rs635441	0.82[CHB][hapmap]
rs647126	0.82[CHB][hapmap]
rs653263	0.80[CHB][hapmap]
rs653529	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs659366	0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs660339	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs673494	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs675547	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7926165	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv1827060	chr11:73670645-73694754	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv1001380	chr11:73680052-73684451	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs655717	MRPL48	cis	lymphoblastoid	seeQTL
rs655717	C2CD3	cis	cerebellum	SCAN
rs655717	PAAF1	cis	lymphoblastoid	seeQTL
rs655717	MRPL48	cis	cerebellum	SCAN
rs655717	UCP2	Cis_1M	lymphoblastoid	RTeQTL
rs655717	UCP2	cis	parietal	SCAN
rs655717	LRRC32	cis	parietal	SCAN
rs655717	PAAF1	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73669000-73685800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:73672800-73684800	Weak transcription	HSMM	muscle
3	chr11:73672800-73693200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:73674000-73685000	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:73675200-73684400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr11:73675200-73685400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr11:73675400-73692600	Weak transcription	Psoas Muscle	Psoas
8	chr11:73675800-73685400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:73675800-73685400	Weak transcription	Fetal Brain Female	brain
10	chr11:73676000-73684400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr11:73676000-73685000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:73676000-73685400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:73676000-73685600	Weak transcription	HepG2	liver
14	chr11:73676000-73686000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:73676000-73686200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:73676000-73686200	Weak transcription	Brain Substantia Nigra	brain
17	chr11:73676000-73686400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:73676000-73687400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:73676200-73685000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr11:73676200-73685000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:73676200-73685200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:73676200-73685400	Weak transcription	Brain Anterior Caudate	brain
23	chr11:73676200-73687600	Weak transcription	Brain Angular Gyrus	brain
24	chr11:73676400-73685400	Weak transcription	Hela-S3	cervix
25	chr11:73676400-73685800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:73676400-73693200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:73676600-73684600	Weak transcription	A549	lung
28	chr11:73676600-73684800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:73676600-73685200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:73676600-73685200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:73676600-73685600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:73676600-73691000	Weak transcription	Fetal Heart	heart
33	chr11:73678200-73685200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr11:73678200-73685200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr11:73678600-73685000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr11:73678600-73685400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:73678600-73685400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr11:73678800-73685200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:73678800-73685600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:73679400-73684600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:73679600-73684400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr11:73679800-73685000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:73680000-73686800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:73680400-73685600	Enhancers	Placenta	Placenta
45	chr11:73680800-73684400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr11:73680800-73685400	Enhancers	K562	blood
47	chr11:73681600-73685000	Weak transcription	Dnd41	blood
48	chr11:73681800-73684400	Weak transcription	Fetal Stomach	stomach
49	chr11:73682400-73685600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:73682400-73685600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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