Variant report

Variant	rs13175367
Chromosome Location	chr5:177037759-177037760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:177037453-177037804	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:177037412-177037938	GM12891	blood:	n/a	n/a
3	POLR2A	chr5:177037541-177039605	GM12891	blood:	n/a	n/a
4	POLR2A	chr5:177035747-177038468	MCF10A-Er-Src	breast:	n/a	n/a
5	ZNF263	chr5:177037434-177038672	HEK293-T-REx	kidney:	n/a	chr5:177037688-177037697 chr5:177037453-177037462
6	POLR2A	chr5:177037568-177038146	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:177037536-177037855	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:177037498-177037877	K562	blood:	n/a	n/a
9	POLR2A	chr5:177037220-177037960	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr5:177037525-177039647	GM12891	blood:	n/a	n/a
11	POLR2A	chr5:177037516-177038453	GM12892	blood:	n/a	n/a
12	POLR2A	chr5:177037526-177038040	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr5:177037318-177040433	GM12892	blood:	n/a	n/a
14	POLR2A	chr5:177037385-177039118	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:177037673-177040836	K562	blood:	n/a	n/a
16	POLR2A	chr5:177037459-177039607	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:177037358-177038797	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr5:177034087-177039636	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr5:177037341-177038563	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr5:177037519-177038069	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:177037628-177037967	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr5:177037496-177039585	A549	lung:	n/a	n/a
23	POLR2A	chr5:177037437-177039761	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr5:177037718-177039473	HCT-116	colon:	n/a	n/a
25	POLR2A	chr5:177037731-177037998	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr5:177037422-177039726	GM12892	blood:	n/a	n/a
27	POLR2A	chr5:177037691-177038694	HCT-116	colon:	n/a	n/a
28	POLR2A	chr5:177035553-177039714	GM12878	blood:	n/a	n/a
29	POLR2A	chr5:177037405-177038962	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr5:177037540-177037908	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr5:177037327-177037926	MCF-7	breast:	n/a	n/a
32	POLR2A	chr5:177037600-177038355	K562	blood:	n/a	n/a
33	POLR2A	chr5:177037488-177039534	HEK293	kidney:	n/a	n/a
34	POLR2A	chr5:177035707-177040321	K562	blood:	n/a	n/a
35	POLR2A	chr5:177037462-177040330	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr5:177037408-177039548	GM12878	blood:	n/a	n/a
37	POLR2A	chr5:177037735-177040257	HepG2	liver:	n/a	n/a
38	POLR2A	chr5:177035720-177039688	HL-60	blood:	n/a	n/a
39	POLR2A	chr5:177037301-177038348	HL-60	blood:	n/a	n/a
40	POLR2A	chr5:177035962-177041711	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

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:

No data

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

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11537644	0.84[ASN][1000 genomes]
rs12515264	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12515554	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169820	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175194	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185565	0.90[EUR][1000 genomes]
rs13187467	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs189243	0.86[ASN][1000 genomes]
rs28499263	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28587776	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28693973	0.86[ASN][1000 genomes]
rs28712028	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2878523	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs337341	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs337362	0.86[ASN][1000 genomes]
rs34457379	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34582406	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34708092	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34857879	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36092039	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364970	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs366470	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs461163	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62398479	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6600989	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs72815179	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7718106	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs834549	0.86[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13175367	B4GALT7	cis	Whole Blood	GTEx
rs13175367	FAM153C	cis	Esophagus Muscularis	GTEx

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	chr5:177034600-177039600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:177034600-177044400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:177034800-177037800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:177034800-177038800	Strong transcription	Fetal Intestine Small	intestine
29	chr5:177034800-177039200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:177034800-177040400	Strong transcription	Fetal Brain Female	brain
31	chr5:177034800-177044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr5:177034800-177044600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:177034800-177045000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:177035000-177037800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:177035000-177038400	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:177035000-177043400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:177035000-177044600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:177035000-177044600	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:177035000-177044600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:177035000-177044600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr5:177035000-177045400	Weak transcription	Pancreas	Pancrea
43	chr5:177035000-177045400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr5:177035000-177045600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:177035000-177046600	Weak transcription	Fetal Brain Male	brain
46	chr5:177035000-177051000	Weak transcription	Stomach Mucosa	stomach
47	chr5:177035000-177054200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:177035200-177037800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:177035200-177038000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:177035200-177038400	Strong transcription	Fetal Intestine Large	intestine

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