Variant report

Variant	rs2272337
Chromosome Location	chr7:99753121-99753122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99751690..99753574-chr7:99764837..99766531,2	MCF-7	breast:
2	chr7:99750795..99756202-chr7:99762627..99766634,7	K562	blood:
3	chr7:99752857..99757651-chr7:99763240..99770051,14	MCF-7	breast:
4	chr7:99696898..99700086-chr7:99750657..99754674,4	MCF-7	breast:
5	chr7:99690528..99692803-chr7:99751485..99754515,3	MCF-7	breast:
6	chr7:99697399..99699503-chr7:99751252..99753483,2	MCF-7	breast:
7	chr7:99751463..99761050-chr7:99772463..99778676,10	K562	blood:
8	chr7:99708863..99711392-chr7:99752836..99754442,2	K562	blood:
9	chr7:99752659..99755597-chr7:99969374..99971671,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000221838	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000085514	Chromatin interaction
ENSG00000207757	Chromatin interaction
ENSG00000208036	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000197093	Chromatin interaction
ENSG00000207547	Chromatin interaction
ENSG00000213420	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10231604	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11764584	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11771167	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12705073	0.90[LWK][hapmap]
rs12878	0.88[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs1527423	0.84[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs1918352	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1918353	0.88[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2272338	0.84[LWK][hapmap]
rs2405440	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35042434	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736590	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736591	0.88[GIH][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs3779047	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800951	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823646	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4134917	0.84[LWK][hapmap]
rs4729577	0.81[LWK][hapmap]
rs705867	0.87[LWK][hapmap]
rs7785392	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7787294	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7787492	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7807641	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs999885	0.81[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
9	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
10	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
11	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
12	nsv888773	chr7:99751594-99772298	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2272337	ZSCAN21	cis	parietal	SCAN
rs2272337	AP4M1	cis	cerebellum	SCAN
rs2272337	AP4M1	cis	Artery Tibial	GTEx
rs2272337	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs2272337	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs2272337	AP4M1	cis	lymphoblastoid	seeQTL
rs2272337	ZKSCAN1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99747400-99753400	Weak transcription	HSMMtube	muscle
2	chr7:99747400-99754600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:99747400-99754600	Weak transcription	Fetal Heart	heart
4	chr7:99747400-99754600	Weak transcription	Right Atrium	heart
5	chr7:99747400-99755200	Weak transcription	Psoas Muscle	Psoas
6	chr7:99747400-99755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:99747600-99753400	Weak transcription	NH-A	brain
8	chr7:99747800-99753400	Weak transcription	Fetal Kidney	kidney
9	chr7:99747800-99754600	Weak transcription	HUVEC	blood vessel
10	chr7:99748000-99753400	Weak transcription	Brain Angular Gyrus	brain
11	chr7:99748000-99755200	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr7:99748200-99753400	Weak transcription	NHDF-Ad	bronchial
13	chr7:99748200-99754200	Weak transcription	Fetal Brain Male	brain
14	chr7:99749000-99754400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr7:99749000-99754400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:99749200-99753800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:99749200-99754400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr7:99749200-99754600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:99749200-99755000	Genic enhancers	Fetal Intestine Large	intestine
20	chr7:99749400-99754200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:99749400-99754200	Strong transcription	Fetal Muscle Leg	muscle
22	chr7:99749400-99754400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr7:99749400-99754400	Genic enhancers	Placenta	Placenta
24	chr7:99749400-99754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:99749400-99754600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:99749400-99754600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr7:99749400-99754600	Strong transcription	Fetal Stomach	stomach
28	chr7:99749400-99754800	Genic enhancers	Fetal Intestine Small	intestine
29	chr7:99749400-99754800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:99749600-99753800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:99749600-99754600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:99749600-99754600	Strong transcription	Brain Anterior Caudate	brain
33	chr7:99749800-99753200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr7:99750000-99754800	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr7:99750200-99753800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:99750200-99754200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:99750200-99754200	Strong transcription	Spleen	Spleen
38	chr7:99750200-99754600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:99750200-99754600	Strong transcription	Osteobl	bone
40	chr7:99750200-99754800	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr7:99750400-99753800	Strong transcription	Fetal Thymus	thymus
42	chr7:99750400-99754200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:99750600-99754000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:99750600-99754200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:99750600-99755200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr7:99750800-99753200	Strong transcription	Dnd41	blood
47	chr7:99750800-99754000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:99750800-99754000	Strong transcription	Thymus	Thymus
49	chr7:99750800-99754000	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr7:99750800-99754400	Genic enhancers	Primary monocytes fromperipheralblood	blood

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