Variant report

Variant	rs3821829
Chromosome Location	chr3:51736644-51736645
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	chr3:51736499-51736667	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:51736587-51736782	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51464596..51467000-chr3:51736520..51738058,2	MCF-7	breast:
2	chr3:51734961..51737149-chr3:51738002..51740092,2	K562	blood:

Variant related genes	Relation type
GRM2	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11917683	0.86[CEU][hapmap]
rs11919197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090011	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234644	0.86[CEU][hapmap]
rs4317086	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4355273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4468965	0.85[EUR][1000 genomes]
rs4687721	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4687734	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4687770	0.92[CEU][hapmap]
rs4687771	0.93[CEU][hapmap]
rs6771491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6787312	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1814919	chr3:51703488-51752684	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv590278	chr3:51724147-51736744	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv590279	chr3:51724147-51737852	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3821829	TEX264	cis	Artery Tibial	GTEx
rs3821829	TEX264	cis	Nerve Tibial	GTEx
rs3821829	TEX264	cis	Stomach	GTEx
rs3821829	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51706400-51741000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:51706600-51739600	Weak transcription	Small Intestine	intestine
3	chr3:51707800-51740400	Strong transcription	Fetal Intestine Small	intestine
4	chr3:51708800-51738800	Strong transcription	Fetal Intestine Large	intestine
5	chr3:51716200-51737000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:51716400-51741200	Weak transcription	Fetal Kidney	kidney
7	chr3:51716800-51738800	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:51717400-51739800	Strong transcription	Liver	Liver
9	chr3:51719600-51741200	Weak transcription	NHDF-Ad	bronchial
10	chr3:51720600-51739800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:51720600-51740000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:51721000-51738200	Weak transcription	A549	lung
13	chr3:51721000-51741000	Weak transcription	HUVEC	blood vessel
14	chr3:51721400-51738800	Strong transcription	Colonic Mucosa	Colon
15	chr3:51721400-51739400	Strong transcription	Thymus	Thymus
16	chr3:51721400-51739800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:51721400-51740000	Strong transcription	Placenta	Placenta
18	chr3:51721400-51740200	Strong transcription	Esophagus	oesophagus
19	chr3:51721400-51740400	Strong transcription	Dnd41	blood
20	chr3:51721400-51740600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:51721400-51740800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:51721600-51739400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:51721600-51740400	Strong transcription	Fetal Stomach	stomach
24	chr3:51721600-51740800	Weak transcription	HSMM	muscle
25	chr3:51721800-51740200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:51722200-51739200	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:51722400-51739000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:51722400-51740200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:51722600-51740000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:51722600-51741200	Weak transcription	Stomach Mucosa	stomach
31	chr3:51723200-51738600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:51723800-51738200	Strong transcription	Fetal Thymus	thymus
33	chr3:51723800-51739400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:51724000-51739000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:51724000-51740200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:51724000-51740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:51724400-51741200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:51725400-51740800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:51725600-51736800	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:51725600-51737000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:51725600-51740000	Strong transcription	Lung	lung
42	chr3:51725600-51740200	Strong transcription	Gastric	stomach
43	chr3:51726200-51738800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:51726400-51737200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:51727000-51739200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:51727400-51740200	Weak transcription	Psoas Muscle	Psoas
47	chr3:51728000-51739600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:51728200-51738800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:51728200-51740200	Strong transcription	Adipose Nuclei	Adipose
50	chr3:51728400-51739400	Strong transcription	Rectal Mucosa Donor 31	rectum

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