Variant report

Variant	rs2272338
Chromosome Location	chr7:99707712-99707713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99707418..99708037-chr7:99728480..99729224,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235077	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs10231604	0.86[LWK][hapmap];0.83[YRI][hapmap]
rs1050542	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1141057	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11550034	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12112428	0.85[ASN][1000 genomes]
rs12112642	0.85[ASN][1000 genomes]
rs12534494	0.85[ASN][1000 genomes]
rs12878	0.94[ASW][hapmap];0.84[CEU][hapmap];0.93[LWK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap]
rs13309	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1527423	0.87[MEX][hapmap]
rs1534309	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1569055	0.83[ASN][1000 genomes]
rs2272337	0.84[LWK][hapmap]
rs2285886	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2293481	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35058708	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35414630	1.00[CHD][hapmap];0.81[JPT][hapmap]
rs3736590	0.84[LWK][hapmap]
rs3736591	0.94[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap]
rs3807479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4134888	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4134917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4134923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729568	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729571	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4729572	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4729577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62485010	0.88[ASN][1000 genomes]
rs62485013	0.83[ASN][1000 genomes]
rs6960432	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941290	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9649220	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs999885	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs999886	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2272338	MBLAC1	cis	cerebellum	SCAN
rs2272338	AP4M1	cis	lymphoblastoid	seeQTL
rs2272338	AP4M1	cis	Artery Tibial	GTEx
rs2272338	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs2272338	AP4M1	cis	Esophagus Muscularis	GTEx
rs2272338	AP4M1	cis	Nerve Tibial	GTEx
rs2272338	TAF6	cis	Thyroid	GTEx
rs2272338	ZSCAN21	cis	parietal	SCAN
rs2272338	ZKSCAN1	cis	multi-tissue	Pritchard
rs2272338	AP4M1	cis	Lymphoblastoid	GTEx
rs2272338	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs2272338	AP4M1	cis	cerebellum	SCAN
rs2272338	GATS	cis	parietal	SCAN
rs2272338	AP4M1	cis	multi-tissue	Pritchard
rs2272338	AP4M1	cis	Adipose Subcutaneous	GTEx
rs2272338	AP4M1	cis	Stomach	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99700200-99709400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr7:99700200-99716200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:99700200-99716400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:99700400-99715800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:99700400-99716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:99700400-99716200	Weak transcription	Psoas Muscle	Psoas
7	chr7:99700400-99716200	Weak transcription	Small Intestine	intestine
8	chr7:99700600-99709200	Weak transcription	HepG2	liver
9	chr7:99700600-99710000	Strong transcription	Left Ventricle	heart
10	chr7:99700600-99711000	Weak transcription	Stomach Mucosa	stomach
11	chr7:99700600-99711400	Strong transcription	Placenta	Placenta
12	chr7:99700600-99712000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:99700600-99712000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:99700600-99712000	Strong transcription	Lung	lung
15	chr7:99700600-99712400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:99700600-99713000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:99700600-99713200	Strong transcription	Fetal Muscle Leg	muscle
18	chr7:99700600-99714600	Strong transcription	Fetal Intestine Small	intestine
19	chr7:99700600-99715200	Strong transcription	Fetal Stomach	stomach
20	chr7:99700600-99716200	Weak transcription	Fetal Brain Male	brain
21	chr7:99700800-99709800	Strong transcription	Ovary	ovary
22	chr7:99700800-99711800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:99700800-99711800	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr7:99700800-99712000	Strong transcription	Brain Cingulate Gyrus	brain
25	chr7:99700800-99712000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr7:99700800-99712200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:99700800-99712200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:99700800-99712600	Strong transcription	Colonic Mucosa	Colon
29	chr7:99700800-99713000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr7:99700800-99713000	Strong transcription	Thymus	Thymus
31	chr7:99700800-99714400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:99701000-99711600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:99701000-99711800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:99701000-99712000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr7:99701000-99712000	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr7:99701000-99712000	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:99701000-99712800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr7:99701000-99712800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:99701000-99712800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr7:99701000-99713000	Strong transcription	Fetal Thymus	thymus
41	chr7:99701000-99713000	Strong transcription	Spleen	Spleen
42	chr7:99701000-99713200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:99701000-99714000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:99701000-99714600	Strong transcription	Fetal Intestine Large	intestine
45	chr7:99701200-99711400	Strong transcription	Pancreas	Pancrea
46	chr7:99701200-99712000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr7:99701200-99712000	Strong transcription	Brain Germinal Matrix	brain
48	chr7:99701200-99712000	Strong transcription	Fetal Brain Female	brain
49	chr7:99701200-99712000	Strong transcription	Gastric	stomach
50	chr7:99701200-99712000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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