Variant report

Variant	rs1678996
Chromosome Location	chr15:42498400-42498401
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	chr15:42498380-42498504	K562	blood:	n/a	n/a
2	POLR2A	chr15:42498275-42498475	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000261002	TF binding region

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10152909	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070363	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12324804	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440779	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12442769	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12915387	0.90[ASN][1000 genomes]
rs12915946	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12917071	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1616957	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1619537	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1626437	1.00[ASN][1000 genomes]
rs1630294	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678987	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678988	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678989	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678990	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679000	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679001	0.98[ASN][1000 genomes]
rs1679008	0.98[ASN][1000 genomes]
rs1679011	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1703748	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703751	0.96[ASN][1000 genomes]
rs1703753	0.98[ASN][1000 genomes]
rs1712390	1.00[ASN][1000 genomes]
rs1712391	0.98[ASN][1000 genomes]
rs1712397	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1712406	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1712407	0.98[ASN][1000 genomes]
rs1712408	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1712409	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1712410	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1712417	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1712420	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1712422	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1712442	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2412671	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412674	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2620378	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620379	0.98[ASN][1000 genomes]
rs2620380	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620381	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2620383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2620387	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2663092	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2663096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2677751	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28767320	0.94[ASN][1000 genomes]
rs2928333	0.98[ASN][1000 genomes]
rs4923934	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4923937	0.85[AFR][1000 genomes]
rs4924633	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924635	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4924636	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924638	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4924640	0.89[AFR][1000 genomes]
rs4924642	0.85[AFR][1000 genomes]
rs4924643	0.89[AFR][1000 genomes]
rs583541	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588695	0.96[ASN][1000 genomes]
rs590540	0.98[ASN][1000 genomes]
rs593910	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598441	0.96[ASN][1000 genomes]
rs599316	0.82[ASN][1000 genomes]
rs602270	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs607959	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs609660	0.96[ASN][1000 genomes]
rs613090	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs613131	0.96[ASN][1000 genomes]
rs613157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614733	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614774	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs615023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs616071	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618161	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs621365	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627478	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629255	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633310	0.90[ASN][1000 genomes]
rs633483	0.98[ASN][1000 genomes]
rs635617	0.98[ASN][1000 genomes]
rs635669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635690	1.00[ASN][1000 genomes]
rs635919	0.98[ASN][1000 genomes]
rs636604	1.00[ASN][1000 genomes]
rs637445	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs641119	0.98[ASN][1000 genomes]
rs644627	1.00[ASN][1000 genomes]
rs645304	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647581	0.98[ASN][1000 genomes]
rs648720	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493026	0.89[AFR][1000 genomes]
rs650910	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs659354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs660033	0.98[ASN][1000 genomes]
rs663454	0.98[ASN][1000 genomes]
rs665262	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665718	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668973	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670329	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670421	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672946	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67384392	0.87[AFR][1000 genomes]
rs677845	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677895	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs683579	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs685521	0.98[ASN][1000 genomes]
rs7164480	0.90[AFR][1000 genomes]
rs7170943	0.89[AFR][1000 genomes]
rs7181577	0.98[ASN][1000 genomes]
rs8023923	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8030650	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8031735	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036917	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8108	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783720	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1054102	chr15:42493052-42528765	Active TSS Strong transcription Weak transcription Enhancers 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	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:133 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42460000-42499200	Weak transcription	A549	lung
2	chr15:42460000-42499800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:42466000-42498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:42475000-42499200	Weak transcription	Stomach Mucosa	stomach
5	chr15:42476800-42499600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:42478400-42498600	Weak transcription	Gastric	stomach
7	chr15:42480400-42498600	Weak transcription	Small Intestine	intestine
8	chr15:42480400-42498800	Weak transcription	Right Ventricle	heart
9	chr15:42481200-42499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:42481600-42498600	Weak transcription	Fetal Brain Male	brain
11	chr15:42482800-42499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:42483200-42499400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:42483400-42498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:42483400-42498600	Weak transcription	Fetal Kidney	kidney
15	chr15:42483600-42498600	Weak transcription	Brain Substantia Nigra	brain
16	chr15:42483600-42498600	Weak transcription	K562	blood
17	chr15:42483600-42499200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:42483800-42499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:42484000-42499200	Weak transcription	HMEC	breast
20	chr15:42484400-42499400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:42484800-42498600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:42484800-42498800	Weak transcription	NHEK	skin
23	chr15:42484800-42499400	Weak transcription	Left Ventricle	heart
24	chr15:42487400-42498400	Weak transcription	HepG2	liver
25	chr15:42490000-42499400	Weak transcription	Aorta	Aorta
26	chr15:42490000-42499400	Weak transcription	Colonic Mucosa	Colon
27	chr15:42490400-42498600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:42490400-42498600	Weak transcription	NHDF-Ad	bronchial
29	chr15:42490800-42498600	Weak transcription	Fetal Intestine Small	intestine
30	chr15:42490800-42499200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:42491000-42499000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:42491000-42499200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:42491000-42499200	Weak transcription	NHLF	lung
34	chr15:42491000-42499400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:42491200-42498600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:42491400-42499200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:42491400-42499200	Weak transcription	NH-A	brain
38	chr15:42491600-42499200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr15:42491800-42498400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:42491800-42498600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:42491800-42499400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:42492000-42498400	Weak transcription	Fetal Brain Female	brain
43	chr15:42492000-42498600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:42492000-42498800	Weak transcription	Ovary	ovary
45	chr15:42492000-42498800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:42492000-42498800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:42492000-42498800	Weak transcription	HSMM	muscle
48	chr15:42492000-42499000	Weak transcription	Hela-S3	cervix
49	chr15:42492000-42499200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:42492000-42499200	Weak transcription	HSMMtube	muscle

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