Variant report

Variant	rs329380
Chromosome Location	chr3:137894077-137894078
allele	G/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	chr3:137893056-137894493	HepG2	liver:	n/a	n/a
2	NFIC	chr3:137893407-137894078	GM12878	blood:	n/a	n/a
3	ELF1	chr3:137893208-137894140	HCT-116	colon:	n/a	chr3:137893773-137893784 chr3:137893774-137893783 chr3:137893773-137893784
4	GABPA	chr3:137893026-137894226	MCF-7	breast:	n/a	n/a
5	ELF1	chr3:137893252-137894120	MCF-7	breast:	n/a	chr3:137893773-137893784 chr3:137893774-137893783 chr3:137893773-137893784
6	GATA3	chr3:137893195-137894186	MCF-7	breast:	n/a	chr3:137893216-137893224
7	ZBTB33	chr3:137893174-137894119	SK-N-SH	brain:	n/a	chr3:137893788-137893798 chr3:137893790-137893799 chr3:137893785-137893800
8	CHD2	chr3:137893097-137894181	Hela-S3	cervix:	n/a	chr3:137893790-137893799
9	CHD2	chr3:137893125-137894087	HepG2	liver:	n/a	chr3:137893790-137893799
10	RFX5	chr3:137893235-137894176	Hela-S3	cervix:	n/a	n/a
11	FOXA2	chr3:137893927-137894157	HepG2	liver:	n/a	n/a
12	CHD2	chr3:137893079-137894215	K562	blood:	n/a	chr3:137893790-137893799
13	POLR2A	chr3:137893217-137894348	GM12892	blood:	n/a	n/a
14	POLR2A	chr3:137892916-137894091	MCF10A-Er-Src	breast:	n/a	n/a
15	ZBTB33	chr3:137893537-137894079	HepG2	liver:	n/a	chr3:137893788-137893798 chr3:137893790-137893799 chr3:137893785-137893800
16	GATA3	chr3:137893224-137894116	A549	lung:	n/a	n/a
17	SIN3AK20	chr3:137893267-137894123	MCF-7	breast:	n/a	n/a
18	HCFC1	chr3:137892983-137894223	Hela-S3	cervix:	n/a	n/a
19	ELF1	chr3:137893233-137894185	HCT-116	colon:	n/a	chr3:137893773-137893784 chr3:137893774-137893783 chr3:137893773-137893784
20	CTCF	chr3:137893960-137894110	GM12801	blood:	n/a	n/a
21	FOXA1	chr3:137893632-137894210	HepG2	liver:	n/a	n/a
22	IRF1	chr3:137893256-137894138	K562	blood:	n/a	chr3:137893393-137893407 chr3:137893773-137893793
23	REST	chr3:137892800-137894121	H1-neurons	neurons:	n/a	chr3:137893711-137893721
24	RCOR1	chr3:137893350-137894088	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:137893135-137894082	MCF-7	breast:	n/a	n/a
26	CHD2	chr3:137893150-137894105	H1-hESC	embryonic stem cell:	n/a	chr3:137893790-137893799
27	CHD2	chr3:137893151-137894240	GM12878	blood:	n/a	chr3:137893790-137893799

No.	Distal block	Cell Line	Cell type
1	chr17:56708248..56710673-chr3:137893303..137894884,2	MCF-7	breast:
2	chr3:137882946..137886396-chr3:137891072..137895118,4	MCF-7	breast:
3	chr3:137891675..137895635-chr3:137902725..137910565,16	MCF-7	breast:
4	chr3:137891989..137894675-chr3:137980214..137982632,2	K562	blood:
5	chr3:137889024..137895470-chr3:137896789..137909029,20	K562	blood:
6	chr3:137890311..137895409-chr3:137904718..137908692,8	MCF-7	breast:

Variant related genes	Relation type
DBR1	TF binding region
ENSG00000138231	Chromatin interaction
ENSG00000114098	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1137760	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712078	0.88[ASN][1000 genomes]
rs12185936	0.83[ASN][1000 genomes]
rs1600697	0.81[EUR][1000 genomes]
rs2219936	0.80[EUR][1000 genomes]
rs2346744	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346745	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622700	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622732	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622733	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622734	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622735	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622736	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622737	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622739	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622740	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622741	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622742	0.82[EUR][1000 genomes]
rs2622743	0.81[EUR][1000 genomes]
rs2622744	0.80[EUR][1000 genomes]
rs2724681	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2724690	0.81[EUR][1000 genomes]
rs2724710	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2724711	0.80[EUR][1000 genomes]
rs2724712	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724725	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724726	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724727	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732839	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs608594	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430414	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7613041	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7632402	0.81[EUR][1000 genomes]
rs774803	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774804	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs774805	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774806	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs774807	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774808	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774809	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774810	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774811	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774812	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774813	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774814	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs811810	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs811811	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827617	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840008	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851548	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2762347	chr3:137851198-137910007	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv998106	chr3:137851198-137934610	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv877536	chr3:137870523-137970907	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs329380	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs329380	A4GNT	cis	Thyroid	GTEx
rs329380	A4GNT	cis	Artery Tibial	GTEx
rs329380	A4GNT	cis	Adipose Subcutaneous	GTEx
rs329380	A4GNT	cis	Nerve Tibial	GTEx
rs329380	DBR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137892200-137894200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:137892200-137894200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:137892200-137894200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:137892200-137894200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:137892200-137894200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:137892200-137894200	Active TSS	Fetal Brain Female	brain
7	chr3:137892200-137894200	Active TSS	Right Atrium	heart
8	chr3:137892200-137894400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:137892400-137894200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:137892400-137894200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:137892400-137894200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr3:137892400-137894200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:137892400-137894200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:137892400-137894200	Active TSS	Colonic Mucosa	Colon
15	chr3:137892400-137894200	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr3:137892400-137894200	Active TSS	A549	lung
17	chr3:137892400-137894200	Active TSS	K562	blood
18	chr3:137892600-137894200	Active TSS	Brain Angular Gyrus	brain
19	chr3:137892600-137894200	Active TSS	Brain Anterior Caudate	brain
20	chr3:137892600-137894200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr3:137892600-137894200	Active TSS	Ovary	ovary
22	chr3:137892600-137894200	Active TSS	Psoas Muscle	Psoas
23	chr3:137892600-137894200	Active TSS	HMEC	breast
24	chr3:137892600-137894200	Active TSS	HSMM	muscle
25	chr3:137892600-137894400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:137892600-137894400	Active TSS	Colon Smooth Muscle	Colon
27	chr3:137892600-137894400	Active TSS	Hela-S3	cervix
28	chr3:137892600-137894400	Active TSS	HepG2	liver
29	chr3:137892800-137894200	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr3:137892800-137894200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr3:137892800-137894200	Active TSS	Fetal Intestine Large	intestine
32	chr3:137892800-137894200	Active TSS	Fetal Intestine Small	intestine
33	chr3:137892800-137894200	Active TSS	Stomach Mucosa	stomach
34	chr3:137892800-137894400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:137893000-137894200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr3:137893000-137894200	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr3:137893000-137894400	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr3:137893200-137894200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:137893200-137894200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr3:137893200-137894200	Active TSS	Fetal Thymus	thymus
41	chr3:137893200-137894200	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr3:137893200-137894200	Active TSS	Thymus	Thymus
43	chr3:137893200-137894200	Active TSS	GM12878-XiMat	blood
44	chr3:137893200-137894200	Active TSS	HSMMtube	muscle
45	chr3:137893200-137894200	Active TSS	HUVEC	blood vessel
46	chr3:137893200-137894400	Active TSS	Rectal Smooth Muscle	rectum
47	chr3:137893400-137894200	Active TSS	Duodenum Mucosa	Duodenum
48	chr3:137893400-137894400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr3:137893400-137894400	Active TSS	Adipose Nuclei	Adipose
50	chr3:137893400-137894400	Active TSS	Stomach Smooth Muscle	stomach

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