Variant report

Variant	rs34582406
Chromosome Location	chr5:177020032-177020033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr5:177018457-177020158	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:177020025-177020035	K562	blood:	n/a	n/a
3	MXI1	chr5:177018324-177020217	SK-N-SH	brain:	n/a	n/a
4	MXI1	chr5:177018808-177020356	IMR90	lung:	n/a	n/a
5	SIN3AK20	chr5:177018512-177020045	MCF-7	breast:	n/a	n/a
6	CUX1	chr5:177018909-177020033	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:176978290..176981747-chr5:177017313..177020640,7	MCF-7	breast:
2	chr5:176943414..176949809-chr5:177018256..177021226,8	MCF-7	breast:
3	chr5:176946312..176949197-chr5:177018379..177020484,2	K562	blood:
4	chr5:176979031..176980967-chr5:177019678..177022578,2	MCF-7	breast:
5	chr5:176959784..176964247-chr5:177018558..177022874,5	MCF-7	breast:
6	chr5:176939485..176941829-chr5:177017923..177020658,4	MCF-7	breast:
7	chr5:176923095..176925209-chr5:177019148..177022259,3	MCF-7	breast:
8	chr5:177019232..177020994-chr5:177656791..177659399,2	K562	blood:
9	chr5:176942293..176944420-chr5:177019101..177021147,2	MCF-7	breast:
10	chr5:176980076..176982423-chr5:177017925..177021146,3	K562	blood:
11	chr5:176936816..176938708-chr5:177019651..177022498,2	MCF-7	breast:
12	chr5:176951222..176953772-chr5:177019144..177020770,2	MCF-7	breast:
13	chr5:177018435..177020960-chr5:177539226..177540753,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMED9	TF binding region
ENSG00000146094	Chromatin interaction
ENSG00000196923	Chromatin interaction
ENSG00000175309	Chromatin interaction
ENSG00000183258	Chromatin interaction
ENSG00000272459	Chromatin interaction
ENSG00000145911	Chromatin interaction
ENSG00000146067	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11537644	0.96[ASN][1000 genomes]
rs12515264	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12515554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13169820	1.00[CEU][hapmap];1.00[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]
rs13175194	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[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]
rs13175367	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]
rs13187467	0.85[EUR][1000 genomes]
rs189243	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28499263	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28587776	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28693973	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28712028	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2878523	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs335485	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs337341	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs337362	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34457379	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34708092	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34857879	0.80[EUR][1000 genomes]
rs36092039	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs364970	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs366470	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs461163	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs461259	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62398479	0.81[EUR][1000 genomes]
rs6600989	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs72815179	0.88[EUR][1000 genomes]
rs7718106	0.81[EUR][1000 genomes]
rs834549	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1022630	chr5:176975746-177028082	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv537966	chr5:176975746-177028082	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv883181	chr5:176978496-177034786	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	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
8	esv3348457	chr5:176995395-177020808	Active TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv883183	chr5:177019379-177030351	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34582406	FAM153C	cis	Esophagus Muscularis	GTEx
rs34582406	B4GALT7	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177018600-177020200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr5:177018600-177020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr5:177018600-177020200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr5:177018600-177020200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:177018600-177020200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:177018600-177020200	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr5:177018600-177020400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr5:177018600-177020400	Active TSS	Rectal Smooth Muscle	rectum
9	chr5:177018600-177020400	Active TSS	HSMMtube	muscle
10	chr5:177018600-177020600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:177018800-177020200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr5:177018800-177020200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr5:177018800-177020200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr5:177018800-177020200	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr5:177018800-177020200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:177018800-177020200	Active TSS	Aorta	Aorta
17	chr5:177018800-177020200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:177018800-177020200	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr5:177018800-177020200	Active TSS	Right Atrium	heart
20	chr5:177018800-177020200	Active TSS	Right Ventricle	heart
21	chr5:177018800-177020200	Active TSS	A549	lung
22	chr5:177018800-177020200	Active TSS	Hela-S3	cervix
23	chr5:177018800-177020200	Active TSS	HMEC	breast
24	chr5:177018800-177020400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:177018800-177020400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr5:177018800-177020400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:177018800-177020400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:177018800-177020400	Active TSS	NH-A	brain
29	chr5:177018800-177020400	Active TSS	NHLF	lung
30	chr5:177018800-177020600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:177019000-177020200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:177019000-177020200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:177019000-177020200	Active TSS	Fetal Intestine Large	intestine
34	chr5:177019000-177020200	Active TSS	HUVEC	blood vessel
35	chr5:177019000-177020200	Active TSS	NHDF-Ad	bronchial
36	chr5:177019000-177020400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr5:177019000-177020400	Active TSS	GM12878-XiMat	blood
38	chr5:177019200-177020200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:177019200-177020200	Active TSS	Esophagus	oesophagus
40	chr5:177019200-177020200	Active TSS	Gastric	stomach
41	chr5:177019200-177020200	Active TSS	Small Intestine	intestine
42	chr5:177019200-177020400	Active TSS	Pancreas	Pancrea
43	chr5:177019200-177020600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
44	chr5:177019400-177020200	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr5:177019400-177020200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr5:177019400-177020200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr5:177019400-177020200	Flanking Active TSS	Fetal Brain Female	brain
48	chr5:177019400-177020400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr5:177019600-177020200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:177019600-177020200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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