Variant report

Variant	rs3735242
Chromosome Location	chr7:99771849-99771850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr7:99771629-99771859	K562	blood:	n/a	n/a
2	RAD21	chr7:99771611-99771871	MCF-7	breast:	n/a	n/a
3	CTCF	chr7:99771700-99771850	GM12875	blood:	n/a	n/a
4	CTCF	chr7:99771720-99771870	GM12872	blood:	n/a	n/a
5	RAD21	chr7:99771602-99771864	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99770423..99772860-chr7:100025787..100027522,2	MCF-7	breast:
2	chr7:99754799..99757162-chr7:99770359..99773122,3	MCF-7	breast:
3	chr7:99767272..99770756-chr7:99771153..99775151,5	MCF-7	breast:
4	chr7:99754722..99756227-chr7:99770103..99772274,2	MCF-7	breast:

No data

Variant related genes	Relation type
GPC2	TF binding region
STAG3	TF binding region
ENSG00000146826	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000213420	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1043915	0.86[CHB][hapmap]
rs1061230	0.86[CHB][hapmap]
rs10953295	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1138417	0.86[CHB][hapmap]
rs11764176	0.86[CHB][hapmap]
rs12666425	0.86[CHB][hapmap]
rs12705073	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1623264	0.86[CHB][hapmap]
rs1624099	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1636975	0.86[CHB][hapmap]
rs1637001	0.86[CHB][hapmap]
rs1727128	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1727129	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1727133	0.86[CHB][hapmap]
rs1727134	0.86[CHB][hapmap];0.93[YRI][hapmap]
rs1727138	0.86[CHB][hapmap]
rs1727140	0.86[CHB][hapmap]
rs1727145	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1859787	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1918353	0.85[JPT][hapmap]
rs2246713	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2405442	0.82[CHB][hapmap]
rs2528900	0.86[CHB][hapmap]
rs2906646	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2950518	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950520	0.86[CHB][hapmap];0.93[YRI][hapmap]
rs3735241	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779045	0.86[CHB][hapmap]
rs4299940	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4729580	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66809776	0.82[ASN][1000 genomes]
rs6948729	0.86[CHB][hapmap]
rs705867	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7794170	0.86[CHB][hapmap]
rs7799441	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7811662	0.86[CHB][hapmap]
rs858502	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs858506	0.86[CHB][hapmap]
rs858510	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs858513	0.86[CHB][hapmap]
rs866500	0.86[CHB][hapmap];0.93[YRI][hapmap]
rs941287	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv5867	chr7:99766774-99799755	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3735242	AP4M1	cis	Thyroid	GTEx
rs3735242	PILRA	cis	parietal	SCAN
rs3735242	C17orf59	trans	cerebellum	SCAN
rs3735242	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs3735242	MBLAC1	cis	cerebellum	SCAN
rs3735242	AP4M1	cis	cerebellum	SCAN
rs3735242	PILRB	cis	cerebellum	SCAN
rs3735242	PILRB	cis	parietal	SCAN
rs3735242	ZKSCAN1	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99766600-99773800	Weak transcription	Hela-S3	cervix
2	chr7:99766800-99774200	Weak transcription	Fetal Lung	lung
3	chr7:99767000-99773200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:99767000-99773800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr7:99767200-99773800	Weak transcription	HSMM	muscle
6	chr7:99767200-99773800	Weak transcription	NH-A	brain
7	chr7:99767200-99774000	Weak transcription	HSMMtube	muscle
8	chr7:99767800-99773600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:99768400-99772800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:99769000-99773400	Weak transcription	Primary T cells from cord blood	blood
11	chr7:99769000-99773800	Weak transcription	K562	blood
12	chr7:99769600-99773200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:99769600-99774200	Weak transcription	HMEC	breast
14	chr7:99769600-99774600	Weak transcription	Ovary	ovary
15	chr7:99769600-99774600	Weak transcription	Right Atrium	heart
16	chr7:99769800-99772800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:99769800-99773800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:99769800-99773800	Weak transcription	HUVEC	blood vessel
19	chr7:99769800-99774000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:99769800-99774200	Weak transcription	Primary B cells from cord blood	blood
21	chr7:99769800-99774200	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:99769800-99774200	Weak transcription	NHDF-Ad	bronchial
23	chr7:99769800-99774600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:99770000-99772200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr7:99770000-99772200	Weak transcription	Fetal Intestine Small	intestine
26	chr7:99770000-99772400	Weak transcription	Fetal Brain Male	brain
27	chr7:99770000-99773400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr7:99770000-99773800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:99770000-99773800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:99770000-99773800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:99770000-99774000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr7:99770000-99774000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr7:99770000-99774200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:99770000-99774200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:99770000-99774200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:99770000-99774200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:99770000-99774200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:99770000-99774200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr7:99770000-99774200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr7:99770000-99774200	Weak transcription	GM12878-XiMat	blood
41	chr7:99770000-99774400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:99770000-99774800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr7:99770000-99774800	Weak transcription	Spleen	Spleen
44	chr7:99770800-99772200	Strong transcription	Fetal Brain Female	brain
45	chr7:99770800-99773000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:99770800-99773200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr7:99771000-99773200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:99771000-99773400	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr7:99771200-99773000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:99771200-99773200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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