Variant report

Variant	rs1727128
Chromosome Location	chr7:99809921-99809922
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99809747-99810052	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOSL2	chr7:99809723-99810045	HepG2	liver:	n/a	n/a
3	MTA3	chr7:99808185-99810079	GM12878	blood:	n/a	n/a
4	RUNX3	chr7:99808398-99809944	GM12878	blood:	n/a	n/a
5	CEBPB	chr7:99808759-99810068	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:99809565-99810395	HepG2	liver:	n/a	n/a
7	EBF1	chr7:99808949-99809979	GM12878	blood:	n/a	n/a
8	POLR2A	chr7:99808425-99810051	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:99806182..99808834-chr7:99809702..99811286,2	MCF-7	breast:
2	chr7:99745511..99748040-chr7:99809267..99811160,3	MCF-7	breast:
3	chr7:99795781..99801540-chr7:99806649..99812120,7	K562	blood:
4	chr7:99806315..99809110-chr7:99809565..99811179,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000239521	TF binding region
ENSG00000188186	Chromatin interaction
ENSG00000066923	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1043915	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs1052482	0.84[AFR][1000 genomes]
rs1061230	0.91[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10953295	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1138417	0.91[CHB][hapmap]
rs11764176	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs12666425	0.91[CHB][hapmap];0.81[YRI][hapmap]
rs12705073	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13230744	0.96[YRI][hapmap]
rs1617502	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1618851	0.84[AFR][1000 genomes]
rs1623264	0.91[CHB][hapmap];0.81[YRI][hapmap]
rs1624099	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636975	0.91[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1637001	0.91[CHB][hapmap];0.82[YRI][hapmap]
rs1727123	0.82[AFR][1000 genomes]
rs1727124	0.82[AFR][1000 genomes]
rs1727129	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727130	0.84[AFR][1000 genomes]
rs1727132	0.82[AFR][1000 genomes]
rs1727133	0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1727134	0.91[CHB][hapmap]
rs1727138	0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1727140	0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1727145	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859787	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1918353	0.85[JPT][hapmap]
rs2005763	0.82[AFR][1000 genomes]
rs2246713	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2405442	0.87[CHB][hapmap]
rs2528900	0.91[CHB][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes]
rs2906646	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950518	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2950520	0.91[CHB][hapmap]
rs3735241	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3735242	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3779045	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs4299940	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729580	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6948729	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs705867	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7794170	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs7799441	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7811662	0.91[CHB][hapmap];0.81[YRI][hapmap]
rs858502	0.94[ASN][1000 genomes]
rs858506	0.91[CHB][hapmap]
rs858510	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858513	0.91[CHB][hapmap]
rs866500	0.91[CHB][hapmap]
rs941287	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	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
6	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
7	nsv8182	chr7:99799816-99879781	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv888774	chr7:99807265-99951315	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv981557	chr7:99808038-99811640	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv16057	chr7:99809377-99937347	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1727128	AP4M1	cis	Artery Tibial	GTEx
rs1727128	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs1727128	AP4M1	cis	Whole Blood	GTEx
rs1727128	AP4M1	cis	Thyroid	GTEx
rs1727128	GATS	cis	multi-tissue	Pritchard
rs1727128	GATS	cis	brain	BrainEAC

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99790000-99817000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr7:99795600-99812200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:99796400-99813000	Weak transcription	Brain Substantia Nigra	brain
4	chr7:99796800-99816800	Weak transcription	Brain Germinal Matrix	brain
5	chr7:99796800-99817000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:99798000-99812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr7:99798200-99811200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:99798600-99810400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:99799000-99816600	Weak transcription	Fetal Brain Female	brain
10	chr7:99800200-99812000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:99801400-99826000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr7:99803000-99810600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:99803000-99816800	Weak transcription	Brain Angular Gyrus	brain
14	chr7:99803200-99813600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr7:99805200-99818400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:99805600-99812800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr7:99806000-99810000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:99806000-99810000	Flanking Active TSS	GM12878-XiMat	blood
19	chr7:99806000-99812400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr7:99806800-99819000	Weak transcription	Fetal Lung	lung
21	chr7:99807200-99828400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:99807200-99847000	Weak transcription	Fetal Kidney	kidney
23	chr7:99807400-99815200	Weak transcription	Pancreas	Pancrea
24	chr7:99807600-99810600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr7:99807600-99818400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:99807800-99812000	Weak transcription	K562	blood
27	chr7:99808000-99815200	Enhancers	Primary B cells from cord blood	blood
28	chr7:99808200-99810000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:99808200-99810000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:99808400-99811000	Strong transcription	Brain Cingulate Gyrus	brain
31	chr7:99808400-99813600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr7:99808800-99811200	Enhancers	Duodenum Mucosa	Duodenum
33	chr7:99808800-99811600	Enhancers	Liver	Liver
34	chr7:99809000-99811400	Enhancers	HepG2	liver
35	chr7:99809000-99813400	Weak transcription	Brain Anterior Caudate	brain
36	chr7:99809000-99817600	Weak transcription	Small Intestine	intestine
37	chr7:99809200-99810000	Strong transcription	Fetal Stomach	stomach
38	chr7:99809200-99810400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr7:99809200-99810600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr7:99809200-99813000	Enhancers	Primary T cells from cord blood	blood
41	chr7:99809200-99817600	Weak transcription	Colonic Mucosa	Colon
42	chr7:99809200-99834800	Weak transcription	HSMMtube	muscle
43	chr7:99809400-99810000	Strong transcription	Fetal Muscle Leg	muscle
44	chr7:99809400-99810800	Weak transcription	Brain Hippocampus Middle	brain
45	chr7:99809400-99810800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr7:99809400-99815000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr7:99809400-99817600	Weak transcription	Spleen	Spleen
48	chr7:99809400-99818200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr7:99809600-99810000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr7:99809600-99810200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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