Variant report

Variant	rs12538287
Chromosome Location	chr7:100471121-100471122
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:100470747-100473785	U87	brain:	n/a	n/a
2	POLR2A	chr7:100470876-100471142	HCT-116	colon:	n/a	n/a
3	POLR2A	chr7:100471040-100471153	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99699125..99701845-chr7:100470033..100472730,2	MCF-7	breast:
2	chr7:100027156..100028676-chr7:100470715..100472560,2	K562	blood:
3	chr7:100423829..100426174-chr7:100471078..100472627,2	K562	blood:
4	chr7:100433319..100435177-chr7:100470244..100472636,2	MCF-7	breast:
5	chr7:100470889..100475047-chr7:100805272..100809585,4	MCF-7	breast:
6	chr7:100285374..100287070-chr7:100470986..100472980,2	K562	blood:
7	chr7:100452256..100454865-chr7:100471094..100473854,2	K562	blood:
8	chr7:100470857..100473840-chr8:103875332..103878147,2	K562	blood:
9	chr7:100274266..100277220-chr7:100470078..100472629,2	K562	blood:
10	chr7:100182521..100184068-chr7:100470982..100473122,2	K562	blood:
11	chr7:100470877..100472471-chr7:100728438..100731050,2	MCF-7	breast:
12	chr7:100448750..100454655-chr7:100469427..100474218,6	MCF-7	breast:

No data

Variant related genes	Relation type
SRRT	TF binding region
ENSG00000236305	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000128564	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000169871	Chromatin interaction
ENSG00000172354	Chromatin interaction
ENSG00000146830	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000146834	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12535629	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075756	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3808356	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3847067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4727468	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6955197	0.90[ASN][1000 genomes]
rs7384255	0.90[ASN][1000 genomes]
rs7782299	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7784933	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7789085	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794216	0.81[EUR][1000 genomes]
rs7800241	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer 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 miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS 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	92 gene(s)	inside rSNPs	diseases
9	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS 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	89 gene(s)	inside rSNPs	diseases
13	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
15	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12538287	LOC402682	cis	multi-tissue	Pritchard
rs12538287	FAM185A	cis	cerebellum	SCAN
rs12538287	TRRAP	cis	cerebellum	SCAN
rs12538287	EPHB4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100461800-100471400	Weak transcription	HepG2	liver
2	chr7:100465600-100471800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:100465600-100471800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:100465600-100471800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr7:100465600-100472000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:100465800-100472000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:100466000-100471600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr7:100466000-100471800	Weak transcription	Fetal Brain Male	brain
9	chr7:100466200-100471600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:100466200-100471600	Weak transcription	Brain Angular Gyrus	brain
11	chr7:100466200-100471600	Weak transcription	Brain Germinal Matrix	brain
12	chr7:100466200-100472000	Weak transcription	Fetal Kidney	kidney
13	chr7:100466400-100471600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr7:100466400-100471600	Weak transcription	Right Atrium	heart
15	chr7:100466400-100471800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:100466400-100471800	Weak transcription	Fetal Heart	heart
17	chr7:100466600-100471400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr7:100466600-100471600	Weak transcription	Fetal Brain Female	brain
19	chr7:100466600-100471800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr7:100466600-100471800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:100466600-100471800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:100466600-100471800	Weak transcription	Primary B cells from cord blood	blood
23	chr7:100466600-100472000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:100466800-100471400	Weak transcription	Stomach Mucosa	stomach
25	chr7:100466800-100471600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr7:100466800-100471600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:100466800-100471800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr7:100467000-100471400	Strong transcription	Fetal Intestine Small	intestine
29	chr7:100467000-100471400	Strong transcription	Fetal Muscle Leg	muscle
30	chr7:100467000-100471400	Strong transcription	Fetal Stomach	stomach
31	chr7:100467000-100471400	Strong transcription	Dnd41	blood
32	chr7:100467000-100471600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:100467000-100471600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:100467000-100471600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:100467000-100471600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr7:100467200-100471600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:100467200-100471800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:100467200-100471800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:100467400-100471600	Strong transcription	Fetal Thymus	thymus
40	chr7:100467600-100471400	Strong transcription	Brain Cingulate Gyrus	brain
41	chr7:100467600-100471600	Strong transcription	HMEC	breast
42	chr7:100467600-100471800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:100467600-100471800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:100467600-100471800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:100467600-100471800	Strong transcription	Fetal Intestine Large	intestine
46	chr7:100467800-100471200	Strong transcription	Lung	lung
47	chr7:100467800-100471400	Strong transcription	K562	blood
48	chr7:100467800-100471600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:100467800-100471600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:100467800-100471600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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