Variant report

Variant	rs17584578
Chromosome Location	chr2:86307624-86307625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86305825..86307788-chr2:86328506..86330182,2	K562	blood:
2	chr2:85956198..85956852-chr2:86306801..86307694,2	MCF-7	breast:
3	chr2:86306434..86308864-chr2:86335264..86337422,3	K562	blood:
4	chr2:86054186..86055161-chr2:86306747..86308111,10	MCF-7	breast:
5	chr2:86054177..86056826-chr2:86305154..86307872,2	MCF-7	breast:
6	chr2:86054263..86055159-chr2:86306734..86307688,8	K562	blood:

Variant related genes	Relation type
ENSG00000132300	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10165327	0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs10168635	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10174095	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10179090	0.87[ASN][1000 genomes]
rs10184159	0.82[AFR][1000 genomes]
rs1019591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036554	0.93[ASN][1000 genomes]
rs10427394	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11899576	0.93[ASN][1000 genomes]
rs12612513	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614260	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12620810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12621992	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12622009	0.94[ASN][1000 genomes]
rs12622715	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs12624126	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13384563	0.91[ASN][1000 genomes]
rs13390702	0.93[ASN][1000 genomes]
rs1559516	0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1561328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026854	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026975	1.00[ASW][hapmap];0.86[LWK][hapmap]
rs17027011	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17618001	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2164879	0.94[ASN][1000 genomes]
rs2241435	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2241437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278085	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278086	0.85[AMR][1000 genomes]
rs2278087	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288121	0.85[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2289237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2303339	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2303340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs311562	0.89[ASN][1000 genomes]
rs311566	0.89[ASN][1000 genomes]
rs311567	0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs34522092	0.88[ASN][1000 genomes]
rs3731819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770066	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770081	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770087	1.00[CEU][hapmap];0.94[ASN][1000 genomes]
rs3770089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3770090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[ASN][1000 genomes]
rs3810827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815840	0.89[ASN][1000 genomes]
rs4832242	0.86[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4832250	0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4832255	0.82[CHD][hapmap]
rs56104203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56326127	0.88[ASN][1000 genomes]
rs56977454	0.88[ASN][1000 genomes]
rs57083584	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57398459	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58186343	0.90[ASN][1000 genomes]
rs58365138	0.88[ASN][1000 genomes]
rs58898686	0.90[ASN][1000 genomes]
rs59835600	0.86[ASN][1000 genomes]
rs59947468	0.85[AMR][1000 genomes]
rs60479377	0.85[AMR][1000 genomes]
rs60649958	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60719866	0.85[AMR][1000 genomes]
rs6750765	0.97[ASN][1000 genomes]
rs6755228	0.82[AFR][1000 genomes]
rs73943946	0.93[ASN][1000 genomes]
rs73947314	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608262	0.92[ASN][1000 genomes]
rs9789563	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9973880	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17584578	MBLAC1	trans	brain	seeQTL
rs17584578	C2orf23	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:86286200-86310400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:86286200-86311200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:86290200-86310800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:86290800-86310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:86290800-86314600	Strong transcription	HMEC	breast
11	chr2:86290800-86318600	Strong transcription	K562	blood
12	chr2:86290800-86322600	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr2:86291000-86311200	Strong transcription	Fetal Brain Female	brain
14	chr2:86291600-86319000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:86291800-86311400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:86291800-86318800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:86292800-86331000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:86294800-86309600	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr2:86295200-86323200	Strong transcription	Fetal Stomach	stomach
20	chr2:86295800-86308400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:86295800-86308600	Strong transcription	Brain Germinal Matrix	brain
22	chr2:86295800-86308600	Strong transcription	NHEK	skin
23	chr2:86296000-86322400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:86299200-86310400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:86299400-86308000	Genic enhancers	Fetal Thymus	thymus
26	chr2:86299400-86308200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:86299800-86308000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:86300000-86318200	Strong transcription	Placenta	Placenta
29	chr2:86300000-86323000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:86300000-86331800	Weak transcription	Stomach Mucosa	stomach
31	chr2:86300400-86307800	Weak transcription	Right Atrium	heart
32	chr2:86300400-86308600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:86300600-86308200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:86300600-86308200	Strong transcription	Rectal Smooth Muscle	rectum
35	chr2:86300800-86309000	Strong transcription	Osteobl	bone
36	chr2:86300800-86310200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:86301200-86318200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:86301400-86307800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:86302800-86307800	Weak transcription	Small Intestine	intestine
40	chr2:86303400-86310400	Strong transcription	Left Ventricle	heart
41	chr2:86304600-86322400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:86304800-86308800	Genic enhancers	A549	lung
43	chr2:86304800-86313400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:86305400-86308200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:86305400-86312400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:86305800-86308200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:86305800-86308400	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr2:86306000-86307800	Enhancers	Liver	Liver
49	chr2:86306000-86308000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr2:86306000-86308000	Enhancers	Psoas Muscle	Psoas

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