Variant report

Variant	rs3821020
Chromosome Location	chr2:85869922-85869923
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	TBP	chr2:85869770-85870055	GM12878	blood:	n/a	n/a
2	EBF1	chr2:85869886-85870160	GM12878	blood:	n/a	n/a
3	RUNX3	chr2:85869892-85870199	GM12878	blood:	n/a	n/a
4	EP300	chr2:85869885-85870100	GM12878	blood:	n/a	n/a
5	RCOR1	chr2:85869760-85870178	GM12878	blood:	n/a	n/a
6	EP300	chr2:85869880-85870196	GM12878	blood:	n/a	n/a
7	RUNX3	chr2:85869886-85870182	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:85869838-85870056	HepG2	liver:	n/a	n/a
9	BCL11A	chr2:85869836-85870191	GM12878	blood:	n/a	chr2:85870000-85870009

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85869158..85870679-chr2:85874969..85877858,2	K562	blood:
2	chr2:85864268..85866624-chr2:85868016..85871094,4	K562	blood:

Variant related genes	Relation type
USP39	TF binding region
ENSG00000168883	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10180770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190428	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10191726	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10302	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1044158	0.82[CHD][hapmap]
rs1124836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13383605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs13418207	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs14242	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs1446669	0.84[JPT][hapmap]
rs1562322	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1992151	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028898	0.84[JPT][hapmap]
rs2043675	0.84[JPT][hapmap]
rs2118176	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2232745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2232747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2232748	0.81[JPT][hapmap]
rs2232750	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2304564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2592551	0.84[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs3827550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6547629	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6733550	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6743051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs699664	0.84[JPT][hapmap]
rs7316	0.83[CHB][hapmap]
rs762684	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3821020	hmm28069	cis	multi-tissue	Pritchard
rs3821020	LOC388969	cis	multi-tissue	Pritchard
rs3821020	VAMP8	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85843800-85876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85844800-85881600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:85845000-85876000	Weak transcription	Right Atrium	heart
4	chr2:85845000-85879800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:85845000-85880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:85845000-85880800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:85845000-85881400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:85845000-85881800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:85845000-85883600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:85845400-85879800	Strong transcription	Lung	lung
11	chr2:85845400-85881000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:85845400-85881400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:85845400-85886400	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:85845600-85881800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:85845600-85882200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr2:85845800-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:85845800-85881600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:85845800-85881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:85846000-85875600	Strong transcription	Primary hematopoietic stem cells	blood
20	chr2:85846000-85880800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:85846000-85881400	Strong transcription	Fetal Stomach	stomach
22	chr2:85846000-85881400	Strong transcription	Fetal Thymus	thymus
23	chr2:85846000-85887000	Strong transcription	Liver	Liver
24	chr2:85846000-85887400	Strong transcription	Fetal Intestine Small	intestine
25	chr2:85846200-85871600	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:85846200-85874600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:85846200-85874600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:85846200-85875000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:85846200-85875200	Strong transcription	Placenta	Placenta
30	chr2:85846200-85879400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:85846200-85879400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:85846200-85880000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:85846200-85880000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:85846200-85880000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr2:85846200-85880600	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr2:85846200-85881200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:85846200-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:85846200-85881400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:85846200-85882000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:85846200-85889400	Strong transcription	Thymus	Thymus
41	chr2:85846400-85879600	Strong transcription	Fetal Intestine Large	intestine
42	chr2:85846400-85880600	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr2:85846600-85875600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr2:85846800-85881400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:85846800-85881600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:85847000-85875000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:85847000-85876200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:85847600-85880000	Strong transcription	Fetal Lung	lung
49	chr2:85847800-85881400	Strong transcription	Dnd41	blood
50	chr2:85848000-85872000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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