Variant report

Variant	rs28730644
Chromosome Location	chr4:99993686-99993687
allele	A/G
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	chr4:99992945-99993718	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99988180..99990204-chr4:99991784..99994054,2	K562	blood:

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

Extended variants
information (count: 128 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10002449	0.81[EUR][1000 genomes]
rs10084896	1.00[GIH][hapmap];0.81[EUR][1000 genomes]
rs17028370	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17028473	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs17028505	0.89[ASW][hapmap];0.96[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs17028758	1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs2051429	0.85[AMR][1000 genomes]
rs28720156	0.83[AMR][1000 genomes]
rs28730581	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730584	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730596	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730601	0.96[EUR][1000 genomes]
rs28730610	0.90[AFR][1000 genomes]
rs28730611	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730617	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730625	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730646	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730649	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894370	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894371	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs29001228	0.83[AMR][1000 genomes]
rs29001338	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001342	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001346	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001348	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001631	0.91[AFR][1000 genomes]
rs4499706	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5003497	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55831712	0.81[EUR][1000 genomes]
rs61431883	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323213	0.81[EUR][1000 genomes]
rs62323214	0.81[EUR][1000 genomes]
rs62323216	0.81[EUR][1000 genomes]
rs62323217	0.81[EUR][1000 genomes]
rs62323230	0.81[EUR][1000 genomes]
rs62323231	0.81[EUR][1000 genomes]
rs62323233	0.81[EUR][1000 genomes]
rs62323234	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323235	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323236	0.81[EUR][1000 genomes]
rs62323237	0.81[EUR][1000 genomes]
rs62323238	0.81[EUR][1000 genomes]
rs62323240	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323241	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323242	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323244	0.81[EUR][1000 genomes]
rs62323245	0.83[AMR][1000 genomes]
rs62323246	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323247	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323248	0.81[EUR][1000 genomes]
rs62323249	0.81[EUR][1000 genomes]
rs62323250	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323251	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323252	0.81[EUR][1000 genomes]
rs62323253	0.81[EUR][1000 genomes]
rs62323254	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323255	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323256	0.81[EUR][1000 genomes]
rs62323257	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323258	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323259	0.81[EUR][1000 genomes]
rs62325160	0.81[EUR][1000 genomes]
rs62325161	0.81[EUR][1000 genomes]
rs62325182	0.81[EUR][1000 genomes]
rs62325183	0.81[EUR][1000 genomes]
rs62325184	0.81[EUR][1000 genomes]
rs62325185	0.81[EUR][1000 genomes]
rs62325186	0.81[EUR][1000 genomes]
rs62325187	0.81[EUR][1000 genomes]
rs62325188	0.81[EUR][1000 genomes]
rs62325189	0.81[EUR][1000 genomes]
rs62325192	0.81[EUR][1000 genomes]
rs62325193	0.81[EUR][1000 genomes]
rs62325194	0.81[EUR][1000 genomes]
rs62325195	0.81[EUR][1000 genomes]
rs62325196	0.81[EUR][1000 genomes]
rs62325197	0.81[EUR][1000 genomes]
rs62325198	0.81[EUR][1000 genomes]
rs62325199	0.81[EUR][1000 genomes]
rs62325200	0.81[EUR][1000 genomes]
rs62325201	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325202	0.81[EUR][1000 genomes]
rs62325203	0.81[EUR][1000 genomes]
rs62325204	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325205	0.81[EUR][1000 genomes]
rs62325206	0.81[EUR][1000 genomes]
rs62325208	0.81[EUR][1000 genomes]
rs62325209	0.81[EUR][1000 genomes]
rs62325210	0.81[EUR][1000 genomes]
rs62325211	0.81[EUR][1000 genomes]
rs62325212	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325213	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325236	0.81[EUR][1000 genomes]
rs62325237	0.81[EUR][1000 genomes]
rs62325238	0.81[EUR][1000 genomes]
rs62325239	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325240	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325241	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325245	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532781	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532792	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532799	0.93[LWK][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap]
rs6819694	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6819724	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6822742	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6823388	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6827292	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897156	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897165	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72897167	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7664906	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7667261	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7679102	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7681427	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7687322	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7688859	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7689911	0.93[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs7699232	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9995869	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28730644	ADH5	cis	multi-tissue	Pritchard
rs28730644	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	chr4:99977200-99994400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:99977400-99994800	Weak transcription	Right Atrium	heart
7	chr4:99977400-99996600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:99977400-99996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:99977400-99997000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:99977600-100008400	Weak transcription	Stomach Mucosa	stomach
11	chr4:99977800-100009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:99978000-100007800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:99979800-99994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:99980000-99995000	Weak transcription	Small Intestine	intestine
15	chr4:99980000-99997000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:99981200-99997000	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:99982400-99995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:99982400-99997000	Weak transcription	Hela-S3	cervix
19	chr4:99982400-100000400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:99982600-99996000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:99982800-99996000	Weak transcription	Gastric	stomach
22	chr4:99982800-100000200	Weak transcription	Psoas Muscle	Psoas
23	chr4:99983000-100004600	Weak transcription	Pancreas	Pancrea
24	chr4:99983200-100000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:99983600-99994400	Weak transcription	Esophagus	oesophagus
27	chr4:99983600-100003400	Weak transcription	Right Ventricle	heart
28	chr4:99983800-99995000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:99984400-99996600	Weak transcription	A549	lung
30	chr4:99985600-100005200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:99985600-100006600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:99986200-99994800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:99987200-100005000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:99987200-100005400	Strong transcription	Dnd41	blood
35	chr4:99987200-100006600	Strong transcription	HSMM	muscle
36	chr4:99987200-100008000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:99987400-100007600	Strong transcription	Fetal Thymus	thymus
38	chr4:99987600-100006000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:99987600-100006600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:99987800-99995800	Strong transcription	Adipose Nuclei	Adipose
41	chr4:99987800-100001000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:99987800-100006800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:99987800-100007000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:99988000-100006800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:99988000-100007000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:99988200-100006400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:99988400-100007000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:99988800-100001800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:99989000-100006600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr4:99989000-100006800	Strong transcription	Primary T cells from cord blood	blood

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