Variant report

Variant	rs11744662
Chromosome Location	chr5:179128706-179128707
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr5:179128565-179128820	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:179128236-179129261	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:179124589-179129396	HepG2	liver:	n/a	n/a
4	ZNF384	chr5:179128487-179128742	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:179128160-179128713	K562	blood:	n/a	n/a
6	POLR2A	chr5:179128601-179128729	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr5:179128028-179128715	GM12892	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179120215..179122887-chr5:179127678..179129697,2	K562	blood:
2	chr5:179123586..179129079-chr5:179129217..179136579,19	MCF-7	breast:
3	chr5:179123960..179129281-chr5:179231995..179235216,8	K562	blood:
4	chr5:179125392..179128992-chr5:179244423..179246560,4	K562	blood:
5	chr5:179127758..179131964-chr5:179232228..179234815,3	MCF-7	breast:
6	chr5:179123960..179129252-chr5:179231413..179236095,7	K562	blood:
7	chr5:179047558..179053114-chr5:179123905..179129187,22	K562	blood:
8	chr5:179128478..179132558-chr5:179135787..179140840,4	MCF-7	breast:
9	chr5:179127269..179130217-chr5:179212553..179215180,2	K562	blood:
10	chr5:179126083..179129267-chr5:179148624..179150852,3	K562	blood:
11	chr5:179049208..179051645-chr5:179125705..179129690,6	MCF-7	breast:
12	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
13	chr5:179100838..179108153-chr5:179124449..179130181,22	K562	blood:
14	chr5:179122873..179128898-chr5:179155888..179164921,20	K562	blood:
15	chr5:179121400..179128828-chr5:179157984..179161377,21	K562	blood:
16	chr5:179045239..179052804-chr5:179123707..179130726,40	K562	blood:

No data

Variant related genes	Relation type
CANX	TF binding region
ENSG00000204659	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000161013	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1019443	0.89[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs10447303	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10447304	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10516146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10794700	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10903245	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12374446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12374485	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12522926	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs12652934	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs13172893	0.89[EUR][1000 genomes]
rs13174472	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13182141	0.84[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13184690	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34329357	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34646062	0.85[CEU][hapmap]
rs34785307	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35320050	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797774	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56227602	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56807514	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62404348	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62406180	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6601073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7444571	0.82[ASN][1000 genomes]
rs7736300	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11744662	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179127000-179129200	Weak transcription	Small Intestine	intestine
2	chr5:179127200-179128800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:179127200-179129600	Enhancers	Spleen	Spleen
4	chr5:179127200-179132600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:179127400-179129200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr5:179127400-179137800	Weak transcription	Aorta	Aorta
7	chr5:179127600-179130000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:179127600-179132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:179127800-179128800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:179127800-179128800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:179127800-179128800	Weak transcription	Ovary	ovary
12	chr5:179127800-179128800	Weak transcription	Right Atrium	heart
13	chr5:179127800-179129000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:179127800-179129000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:179127800-179129000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:179127800-179129000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:179127800-179129000	Weak transcription	Brain Germinal Matrix	brain
18	chr5:179127800-179129000	Weak transcription	Fetal Brain Male	brain
19	chr5:179127800-179129000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:179127800-179129000	Weak transcription	HSMM	muscle
21	chr5:179127800-179129200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:179127800-179129200	Enhancers	Primary hematopoietic stem cells	blood
23	chr5:179127800-179129200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:179127800-179129200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr5:179127800-179129200	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr5:179127800-179129200	Enhancers	Right Ventricle	heart
27	chr5:179127800-179129400	Genic enhancers	Fetal Thymus	thymus
28	chr5:179127800-179129600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:179127800-179129600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr5:179127800-179129600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:179127800-179129600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr5:179127800-179129600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr5:179127800-179129600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:179127800-179129600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr5:179127800-179129600	Weak transcription	Fetal Kidney	kidney
36	chr5:179127800-179129600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr5:179127800-179129600	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr5:179127800-179129800	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr5:179127800-179129800	Enhancers	Adipose Nuclei	Adipose
40	chr5:179127800-179129800	Enhancers	Fetal Heart	heart
41	chr5:179127800-179129800	Genic enhancers	HUVEC	blood vessel
42	chr5:179127800-179130200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:179127800-179130200	Weak transcription	Fetal Lung	lung
44	chr5:179127800-179130400	Enhancers	Left Ventricle	heart
45	chr5:179127800-179130400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr5:179127800-179130600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:179127800-179130600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:179127800-179130600	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:179127800-179130600	Weak transcription	Thymus	Thymus
50	chr5:179127800-179130600	Strong transcription	NHLF	lung

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