Variant report

Variant	rs36092039
Chromosome Location	chr5:177036256-177036257
allele	C/T
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	chr5:177035652-177037106	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:177035747-177038468	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:177036038-177036353	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:177035512-177037140	HEK293	kidney:	n/a	n/a
5	POLR2A	chr5:177036217-177037239	MCF-7	breast:	n/a	n/a
6	POLR2A	chr5:177035960-177036494	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:177035717-177037202	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:177035852-177037292	HL-60	blood:	n/a	n/a
9	POLR2A	chr5:177034087-177039636	SK-N-MC	brain:	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	chr5:177036068-177036526	GM12892	blood:	n/a	n/a
13	POLR2A	chr5:177036052-177036299	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr5:177035903-177037249	GM12892	blood:	n/a	n/a
15	POLR2A	chr5:177035707-177040321	K562	blood:	n/a	n/a
16	POLR2A	chr5:177036068-177037192	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr5:177035720-177039688	HL-60	blood:	n/a	n/a
18	POLR2A	chr5:177036017-177036942	GM12892	blood:	n/a	n/a
19	POLR2A	chr5:177036241-177036318	ProgFib	skin:	n/a	n/a
20	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:

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

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11537644	0.84[ASN][1000 genomes]
rs12515264	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12515554	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169820	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175194	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175367	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185565	0.90[EUR][1000 genomes]
rs13187467	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs189243	0.86[ASN][1000 genomes]
rs28499263	0.85[ASN][1000 genomes]
rs28587776	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28693973	0.86[ASN][1000 genomes]
rs28712028	0.82[ASN][1000 genomes]
rs2878523	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs337341	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs337362	0.86[ASN][1000 genomes]
rs34457379	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34582406	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34708092	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34857879	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs364970	0.86[ASN][1000 genomes]
rs366470	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs461163	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62398479	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72815179	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7718106	0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs36092039	RP11-1277A3.2	cis	Nerve Tibial	GTEx
rs36092039	B4GALT7	cis	Whole Blood	GTEx
rs36092039	FAM153C	cis	Esophagus Muscularis	GTEx

Chromatin state (count:118 , 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	chr5:177028200-177036400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:177028200-177038000	Weak transcription	Right Atrium	heart
4	chr5:177028400-177036600	Weak transcription	HMEC	breast
5	chr5:177028400-177040200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:177028400-177042600	Weak transcription	Primary B cells from cord blood	blood
7	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
9	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
10	chr5:177028400-177048400	Weak transcription	NH-A	brain
11	chr5:177028600-177041200	Weak transcription	Fetal Lung	lung
12	chr5:177028600-177046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:177028600-177049000	Weak transcription	HUVEC	blood vessel
14	chr5:177028600-177053200	Weak transcription	HSMM	muscle
15	chr5:177028800-177044600	Weak transcription	GM12878-XiMat	blood
16	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
17	chr5:177029200-177045600	Weak transcription	Brain Angular Gyrus	brain
18	chr5:177030400-177039400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:177032000-177038800	Strong transcription	Dnd41	blood
20	chr5:177032800-177036400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:177032800-177045600	Weak transcription	HSMMtube	muscle
22	chr5:177033000-177045600	Weak transcription	Aorta	Aorta
23	chr5:177033200-177038600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr5:177034000-177037200	Genic enhancers	Spleen	Spleen
25	chr5:177034200-177037000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:177034200-177040400	Strong transcription	Thymus	Thymus
27	chr5:177034400-177045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:177034400-177046200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:177034400-177048600	Weak transcription	A549	lung
30	chr5:177034600-177036600	Weak transcription	Ovary	ovary
31	chr5:177034600-177036600	Strong transcription	Osteobl	bone
32	chr5:177034600-177037400	Strong transcription	Placenta	Placenta
33	chr5:177034600-177039600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:177034600-177044400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:177034800-177036400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr5:177034800-177036400	Weak transcription	Liver	Liver
37	chr5:177034800-177036600	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr5:177034800-177037000	Strong transcription	NHLF	lung
39	chr5:177034800-177037800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:177034800-177038800	Strong transcription	Fetal Intestine Small	intestine
41	chr5:177034800-177039200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:177034800-177040400	Strong transcription	Fetal Brain Female	brain
43	chr5:177034800-177044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:177034800-177044600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:177034800-177045000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:177035000-177036400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:177035000-177036400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:177035000-177036400	Weak transcription	Adipose Nuclei	Adipose
50	chr5:177035000-177036800	Weak transcription	Colonic Mucosa	Colon

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