Variant report

Variant	rs7669660
Chromosome Location	chr4:99992602-99992603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:99987204-99993723	K562	blood:	n/a	n/a
2	POLR2A	chr4:99992433-99992665	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr4:99992470-99992803	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:99992145-99992774	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr4:99992388-99992625	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:99923798..99925569-chr4:99990662..99993574,2	K562	blood:
2	chr4:99988180..99990204-chr4:99991784..99994054,2	K562	blood:
3	chr4:99984530..99987339-chr4:99990898..99992743,2	K562	blood:

Variant related genes	Relation type
ENSG00000272777	TF binding region
ENSG00000272777	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1154400	0.84[ASW][hapmap];0.83[LWK][hapmap];0.83[YRI][hapmap]
rs1154401	0.91[YRI][hapmap]
rs11547772	0.82[AMR][1000 genomes]
rs12106	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1230155	0.84[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1311620	0.91[YRI][hapmap]
rs28730602	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730632	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699700	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658118	0.82[AMR][1000 genomes]
rs7658279	0.82[AMR][1000 genomes]
rs7683704	0.91[ASW][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7684735	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats 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 miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7669660	ADH5	cis	cerebellum	SCAN
rs7669660	MTTP	cis	parietal	SCAN
rs7669660	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99954000-99999200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:99956200-99995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:99959800-100000200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:99971800-99997600	Weak transcription	Spleen	Spleen
5	chr4:99974000-99993000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:99976400-99992800	Weak transcription	Aorta	Aorta
7	chr4:99977200-99994400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:99977400-99992800	Weak transcription	Brain Substantia Nigra	brain
9	chr4:99977400-99994800	Weak transcription	Right Atrium	heart
10	chr4:99977400-99996600	Weak transcription	Brain Angular Gyrus	brain
11	chr4:99977400-99996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:99977400-99997000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:99977600-100008400	Weak transcription	Stomach Mucosa	stomach
14	chr4:99977800-100009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:99978000-100007800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:99979800-99992800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:99979800-99994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:99980000-99993000	Weak transcription	Ovary	ovary
19	chr4:99980000-99995000	Weak transcription	Small Intestine	intestine
20	chr4:99980000-99997000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:99980200-99993000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:99981200-99997000	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:99982400-99995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:99982400-99997000	Weak transcription	Hela-S3	cervix
25	chr4:99982400-100000400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:99982600-99996000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:99982800-99993000	Weak transcription	Left Ventricle	heart
28	chr4:99982800-99996000	Weak transcription	Gastric	stomach
29	chr4:99982800-100000200	Weak transcription	Psoas Muscle	Psoas
30	chr4:99983000-100004600	Weak transcription	Pancreas	Pancrea
31	chr4:99983200-99992800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:99983200-100000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:99983400-99992800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:99983400-99993000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:99983600-99993000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:99983600-99994400	Weak transcription	Esophagus	oesophagus
38	chr4:99983600-100003400	Weak transcription	Right Ventricle	heart
39	chr4:99983800-99995000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:99984400-99996600	Weak transcription	A549	lung
41	chr4:99985600-100005200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:99985600-100006600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:99986200-99994800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:99987200-100005000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:99987200-100005400	Strong transcription	Dnd41	blood
46	chr4:99987200-100006600	Strong transcription	HSMM	muscle
47	chr4:99987200-100008000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:99987400-100007600	Strong transcription	Fetal Thymus	thymus
49	chr4:99987600-100006000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:99987600-100006600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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