Variant report

Variant	rs747861
Chromosome Location	chr5:177037397-177037398
allele	C/G
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	POLR2A	chr5:177035747-177038468	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:177037220-177037960	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr5:177037318-177040433	GM12892	blood:	n/a	n/a
4	POLR2A	chr5:177037385-177039118	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:177037358-177038797	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:177034087-177039636	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr5:177037341-177038563	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr5:177037383-177037408	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr5:177037305-177037657	K562	blood:	n/a	n/a
10	POLR2A	chr5:177035936-177037420	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr5:177035553-177039714	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:177037327-177037926	MCF-7	breast:	n/a	n/a
13	POLR2A	chr5:177035707-177040321	K562	blood:	n/a	n/a
14	POLR2A	chr5:177035720-177039688	HL-60	blood:	n/a	n/a
15	POLR2A	chr5:177037301-177038348	HL-60	blood:	n/a	n/a
16	POLR2A	chr5:177035962-177041711	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:176923645..176926507-chr5:177035246..177038118,2	MCF-7	breast:
2	chr5:177032232..177035500-chr5:177036959..177040383,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247679	TF binding region
ENSG00000196923	Chromatin interaction
ENSG00000027847	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10045871	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10078930	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10479521	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11545868	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11960689	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12651744	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12656594	0.89[EUR][1000 genomes]
rs28534743	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28738071	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs335487	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34705130	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4976703	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6876792	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7710333	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7717102	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7720519	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7729422	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7731640	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9329062	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs968406	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028000-177040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:177028200-177038000	Weak transcription	Right Atrium	heart
3	chr5:177028400-177040200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:177028400-177042600	Weak transcription	Primary B cells from cord blood	blood
5	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
7	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
8	chr5:177028400-177048400	Weak transcription	NH-A	brain
9	chr5:177028600-177041200	Weak transcription	Fetal Lung	lung
10	chr5:177028600-177046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:177028600-177049000	Weak transcription	HUVEC	blood vessel
12	chr5:177028600-177053200	Weak transcription	HSMM	muscle
13	chr5:177028800-177044600	Weak transcription	GM12878-XiMat	blood
14	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
15	chr5:177029200-177045600	Weak transcription	Brain Angular Gyrus	brain
16	chr5:177030400-177039400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:177032000-177038800	Strong transcription	Dnd41	blood
18	chr5:177032800-177045600	Weak transcription	HSMMtube	muscle
19	chr5:177033000-177045600	Weak transcription	Aorta	Aorta
20	chr5:177033200-177038600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:177034200-177040400	Strong transcription	Thymus	Thymus
22	chr5:177034400-177045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:177034400-177046200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:177034400-177048600	Weak transcription	A549	lung
25	chr5:177034600-177037400	Strong transcription	Placenta	Placenta
26	chr5:177034600-177039600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:177034600-177044400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr5:177034800-177037800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:177034800-177038800	Strong transcription	Fetal Intestine Small	intestine
30	chr5:177034800-177039200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:177034800-177040400	Strong transcription	Fetal Brain Female	brain
32	chr5:177034800-177044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr5:177034800-177044600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:177034800-177045000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:177035000-177037400	Strong transcription	Fetal Muscle Leg	muscle
37	chr5:177035000-177037800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:177035000-177038400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:177035000-177043400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:177035000-177044600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:177035000-177044600	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:177035000-177044600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:177035000-177044600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:177035000-177045400	Weak transcription	Pancreas	Pancrea
45	chr5:177035000-177045400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr5:177035000-177045600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:177035000-177046600	Weak transcription	Fetal Brain Male	brain
48	chr5:177035000-177051000	Weak transcription	Stomach Mucosa	stomach
49	chr5:177035000-177054200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr5:177035200-177037800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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