Variant report

Variant	rs7678401
Chromosome Location	chr4:106391880-106391881
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:106066483..106069673-chr4:106390838..106393733,3	K562	blood:
2	chr4:106060523..106062575-chr4:106390965..106392720,2	K562	blood:
3	chr4:106065001..106068039-chr4:106390236..106392618,4	MCF-7	breast:
4	chr4:106391240..106392982-chr4:106630165..106631896,2	K562	blood:
5	chr4:106270792..106273529-chr4:106390596..106392898,2	K562	blood:
6	chr4:106046108..106050165-chr4:106391446..106394724,4	MCF-7	breast:
7	chr4:106060470..106063103-chr4:106391322..106393340,2	K562	blood:
8	chr4:106064984..106068563-chr4:106391196..106395238,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000251259	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10007134	0.98[ASN][1000 genomes]
rs10020998	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10024331	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1125254	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11934602	0.92[ASN][1000 genomes]
rs11934709	0.92[ASN][1000 genomes]
rs2023840	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2046880	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2298732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][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]
rs2636693	0.87[CHB][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap]
rs2636694	0.87[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap]
rs2636747	0.83[ASN][1000 genomes]
rs2713826	0.84[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2866883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs34248474	0.87[CHB][hapmap];0.90[CHD][hapmap];0.93[MEX][hapmap]
rs35775499	0.99[ASN][1000 genomes]
rs3864225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235414	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4699176	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4699178	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6533196	0.92[ASN][1000 genomes]
rs6533197	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6533198	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6533199	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6533201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6816997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6836448	0.94[ASN][1000 genomes]
rs763289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7691192	0.94[ASN][1000 genomes]
rs8180199	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981136	0.94[ASN][1000 genomes]
rs9990819	0.98[ASN][1000 genomes]
rs9999896	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002228	chr4:106346206-106433381	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7678401	PPA2	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106347600-106392800	Weak transcription	Colonic Mucosa	Colon
2	chr4:106348200-106393000	Weak transcription	Thymus	Thymus
3	chr4:106355400-106393200	Weak transcription	Esophagus	oesophagus
4	chr4:106357200-106392600	Weak transcription	Brain Angular Gyrus	brain
5	chr4:106357600-106392200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:106362200-106392600	Weak transcription	A549	lung
7	chr4:106364600-106392000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:106364600-106392600	Weak transcription	Fetal Kidney	kidney
9	chr4:106366000-106392400	Weak transcription	Osteobl	bone
10	chr4:106366000-106392600	Weak transcription	Psoas Muscle	Psoas
11	chr4:106366600-106392200	Weak transcription	Liver	Liver
12	chr4:106366600-106392200	Weak transcription	HepG2	liver
13	chr4:106366600-106392600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:106366800-106393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:106368200-106392000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:106370000-106392600	Weak transcription	HUVEC	blood vessel
17	chr4:106373200-106392600	Weak transcription	NH-A	brain
18	chr4:106373400-106392200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:106374000-106392400	Weak transcription	NHDF-Ad	bronchial
20	chr4:106374000-106393000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:106374600-106392400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:106374600-106392600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:106375400-106392600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:106375400-106393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:106375400-106393000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:106376800-106392600	Weak transcription	Fetal Lung	lung
27	chr4:106377000-106393000	Weak transcription	Right Atrium	heart
28	chr4:106377000-106393200	Weak transcription	Pancreas	Pancrea
29	chr4:106377000-106394000	Weak transcription	Gastric	stomach
30	chr4:106378000-106392200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:106378000-106392200	Weak transcription	HMEC	breast
32	chr4:106378000-106392400	Weak transcription	HSMM	muscle
33	chr4:106378000-106393000	Weak transcription	HSMMtube	muscle
34	chr4:106379200-106392200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:106379200-106392600	Weak transcription	Aorta	Aorta
36	chr4:106379600-106392200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:106381200-106394000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:106381600-106392600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:106382000-106392400	Weak transcription	Brain Substantia Nigra	brain
40	chr4:106382800-106392600	Weak transcription	Stomach Mucosa	stomach
41	chr4:106382800-106392800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:106383200-106392400	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:106383400-106392400	Weak transcription	Fetal Heart	heart
44	chr4:106383400-106393000	Weak transcription	Fetal Brain Female	brain
45	chr4:106385000-106394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:106385200-106393400	Weak transcription	Brain Germinal Matrix	brain
47	chr4:106385400-106392400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:106386400-106394200	Weak transcription	Spleen	Spleen
49	chr4:106386600-106392600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:106388200-106392400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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