Variant report

Variant	rs6547629
Chromosome Location	chr2:85860228-85860229
allele	A/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	chr2:85859807-85860256	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85860109..85864294-chr2:85864823..85868002,4	K562	blood:
2	chr2:85845054..85846904-chr2:85859258..85861801,2	MCF-7	breast:
3	chr2:85858432..85860291-chr2:85861960..85864118,2	K562	blood:

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

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10180770	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10182351	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10187424	0.80[JPT][hapmap]
rs10198569	0.80[JPT][hapmap]
rs10206961	0.85[GIH][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap]
rs1044158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1078004	0.80[JPT][hapmap]
rs1124836	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs12463933	0.85[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs13383605	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs13406807	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17026396	0.80[JPT][hapmap]
rs2028900	0.80[JPT][hapmap]
rs2040349	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs2044474	0.80[JPT][hapmap]
rs2118177	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs2232745	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2232747	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2232748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2232750	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2304564	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs3755015	0.80[JPT][hapmap]
rs3821020	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs3827550	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs58588820	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62166774	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6547621	0.80[JPT][hapmap]
rs6643	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6705971	0.80[JPT][hapmap]
rs6733550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6738645	0.80[JPT][hapmap]
rs6743051	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs7568458	0.80[JPT][hapmap]
rs9678632	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9752	0.86[EUR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6547629	VAMP8	cis	uninvolved skin	skin_eQTL
rs6547629	VAMP8	cis	lymphoblastoid	seeQTL
rs6547629	GGCX	cis	parietal	SCAN
rs6547629	USP39	cis	Liver	GTEx
rs6547629	hmm28069	cis	multi-tissue	Pritchard
rs6547629	GGCX	cis	cerebellum	SCAN

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	chr2:85844800-85862600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:85844800-85881600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:85845000-85876000	Weak transcription	Right Atrium	heart
5	chr2:85845000-85879800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:85845000-85880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:85845000-85880800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:85845000-85881400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:85845000-85881800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:85845000-85883600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:85845400-85864600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:85845400-85879800	Strong transcription	Lung	lung
13	chr2:85845400-85881000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:85845400-85881400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:85845400-85886400	Strong transcription	Fetal Muscle Leg	muscle
16	chr2:85845600-85881800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:85845600-85882200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr2:85845800-85860800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:85845800-85865000	Strong transcription	NH-A	brain
20	chr2:85845800-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:85845800-85881600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:85845800-85881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:85846000-85875600	Strong transcription	Primary hematopoietic stem cells	blood
24	chr2:85846000-85880800	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:85846000-85881400	Strong transcription	Fetal Stomach	stomach
26	chr2:85846000-85881400	Strong transcription	Fetal Thymus	thymus
27	chr2:85846000-85887000	Strong transcription	Liver	Liver
28	chr2:85846000-85887400	Strong transcription	Fetal Intestine Small	intestine
29	chr2:85846200-85864200	Strong transcription	Brain Germinal Matrix	brain
30	chr2:85846200-85871600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:85846200-85874600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:85846200-85874600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:85846200-85875000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:85846200-85875200	Strong transcription	Placenta	Placenta
35	chr2:85846200-85879400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:85846200-85879400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:85846200-85880000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:85846200-85880000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:85846200-85880000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr2:85846200-85880600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr2:85846200-85881200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:85846200-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:85846200-85881400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:85846200-85882000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:85846200-85889400	Strong transcription	Thymus	Thymus
46	chr2:85846400-85864600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:85846400-85864800	Strong transcription	Primary B cells from cord blood	blood
48	chr2:85846400-85869200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:85846400-85879600	Strong transcription	Fetal Intestine Large	intestine
50	chr2:85846400-85880600	Strong transcription	H9 Cell Line	embryonic stem cell

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