Variant report

Variant	rs4729567
Chromosome Location	chr7:99637242-99637243
allele	A/G
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:1)
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	chr7:99636083..99637588-chr7:99637979..99639620,2	K562	blood:
2	chr7:99634823..99637646-chr7:99648903..99650452,2	K562	blood:
3	chr7:99634010..99640137-chr7:99643841..99648236,8	K562	blood:
4	chr7:99612213..99613947-chr7:99635282..99637746,3	K562	blood:
5	chr7:99631794..99640933-chr7:99644912..99651639,12	K562	blood:
6	chr7:99633170..99637307-chr7:99685245..99688799,3	K562	blood:
7	chr7:99613150..99615882-chr7:99635213..99637801,4	MCF-7	breast:
8	chr7:99635895..99638032-chr7:99640487..99642322,2	MCF-7	breast:
9	chr7:99634660..99636728-chr7:99636829..99638955,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZSCAN21-2	chr7:99637173-99639311	NONHSAT122291

No data

Variant related genes	Relation type
ENSG00000168090	Chromatin interaction
ENSG00000166529	Chromatin interaction
ENSG00000106261	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1050542	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1141057	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11550034	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11771331	0.93[YRI][hapmap]
rs12112428	0.96[ASN][1000 genomes]
rs12112642	0.96[ASN][1000 genomes]
rs12534494	0.96[ASN][1000 genomes]
rs12705070	0.86[YRI][hapmap]
rs12878	0.84[CEU][hapmap]
rs13236456	0.80[EUR][1000 genomes]
rs13309	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1527423	0.87[MEX][hapmap]
rs1534309	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2272338	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]
rs2285886	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs2293481	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34161112	0.84[ASN][1000 genomes]
rs35058708	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35414630	1.00[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs3807479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4134888	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4134917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[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]
rs4134923	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4424195	0.86[YRI][hapmap]
rs4729566	0.93[YRI][hapmap]
rs4729568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729571	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729572	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729577	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];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62485010	0.88[ASN][1000 genomes]
rs62485013	0.83[ASN][1000 genomes]
rs6960432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7788746	0.93[YRI][hapmap]
rs7807641	0.83[YRI][hapmap]
rs941290	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9649220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs999885	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs999886	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1824630	chr7:99614770-99639445	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4729567	AP4M1	cis	Stomach	GTEx
rs4729567	TAF6	cis	Thyroid	GTEx
rs4729567	AP4M1	cis	lymphoblastoid	seeQTL
rs4729567	MBLAC1	cis	cerebellum	SCAN
rs4729567	AP4M1	cis	Artery Tibial	GTEx
rs4729567	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs4729567	ZKSCAN1	cis	multi-tissue	Pritchard
rs4729567	ZSCAN21	cis	parietal	SCAN
rs4729567	AP4M1	cis	Esophagus Muscularis	GTEx
rs4729567	AP4M1	cis	Nerve Tibial	GTEx
rs4729567	ZSCAN21	cis	lymphoblastoid	seeQTL
rs4729567	AP4M1	cis	cerebellum	SCAN
rs4729567	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs4729567	GATS	cis	parietal	SCAN
rs4729567	SMURF1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99614200-99639000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99615200-99637800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:99615400-99639600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:99629200-99637800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:99629600-99638200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:99629600-99639000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:99631800-99647000	Weak transcription	Colonic Mucosa	Colon
8	chr7:99632200-99637600	Weak transcription	Aorta	Aorta
9	chr7:99632200-99639000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:99632400-99640200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:99632600-99637800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:99632600-99646600	Weak transcription	Fetal Heart	heart
13	chr7:99632800-99638200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr7:99633000-99638400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:99633000-99646600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:99633600-99638200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:99633600-99638200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:99633600-99639000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:99633600-99639200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:99633600-99640200	Weak transcription	Lung	lung
21	chr7:99633600-99641800	Weak transcription	Spleen	Spleen
22	chr7:99633600-99646400	Weak transcription	Pancreas	Pancrea
23	chr7:99633600-99646600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:99633600-99646600	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:99633600-99646600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr7:99633600-99646600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr7:99633600-99646800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:99633600-99646800	Weak transcription	Psoas Muscle	Psoas
29	chr7:99633600-99647000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:99633800-99637800	Weak transcription	Brain Angular Gyrus	brain
31	chr7:99633800-99638000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:99633800-99638000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:99633800-99646400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:99633800-99646400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr7:99633800-99646600	Weak transcription	Esophagus	oesophagus
36	chr7:99633800-99646600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:99633800-99647000	Weak transcription	Gastric	stomach
38	chr7:99634000-99638200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:99634000-99638200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr7:99634000-99638400	Weak transcription	Primary B cells from cord blood	blood
41	chr7:99634000-99639000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr7:99634000-99646600	Weak transcription	HMEC	breast
43	chr7:99634000-99647000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:99634000-99647000	Weak transcription	Left Ventricle	heart
45	chr7:99634000-99647000	Weak transcription	NHLF	lung
46	chr7:99634200-99638000	Weak transcription	Brain Anterior Caudate	brain
47	chr7:99634200-99646600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:99634200-99647000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:99634400-99640200	Enhancers	Liver	Liver
50	chr7:99634800-99638200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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