Variant report

Variant	rs1539437
Chromosome Location	chr1:114334690-114334691
allele	G/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114333022..114334789-chr1:114335589..114337736,3	K562	blood:
2	chr1:114301004..114303361-chr1:114333727..114335716,2	MCF-7	breast:
3	chr1:114332261..114335677-chr1:114340949..114344053,3	K562	blood:
4	chr1:114329880..114331707-chr1:114332071..114335621,3	K562	blood:
5	chr1:114332999..114335682-chr1:114345986..114348976,2	K562	blood:
6	chr1:114334277..114335869-chr20:50684813..50686450,2	MCF-7	breast:
7	chr1:114333134..114336494-chr1:114338300..114342659,7	MCF-7	breast:
8	chr1:114317996..114324872-chr1:114329159..114335059,8	K562	blood:
9	chr1:114300794..114303535-chr1:114333161..114335881,2	MCF-7	breast:
10	chr1:114324961..114329121-chr1:114330799..114335017,4	K562	blood:
11	chr1:114323968..114327770-chr1:114333801..114338657,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10858016	0.89[ASN][1000 genomes]
rs1111695	0.89[ASN][1000 genomes]
rs1217375	0.80[AFR][1000 genomes]
rs1217378	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217385	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1217404	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1217405	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217406	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217409	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1217411	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217418	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1217419	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1217420	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1230682	1.00[ASN][1000 genomes]
rs1230686	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1235005	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1310182	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273758	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2476600	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2476604	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2797414	1.00[ASN][1000 genomes]
rs2797416	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789598	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789600	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4991898	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537798	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6665194	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6672018	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7555634	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556622	0.89[ASN][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers 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 target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:114311000-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:114311000-114336800	Weak transcription	Fetal Kidney	kidney
5	chr1:114311000-114341800	Weak transcription	Esophagus	oesophagus
6	chr1:114319800-114352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:114320000-114336200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:114320000-114340000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:114320200-114337200	Weak transcription	Placenta	Placenta
11	chr1:114320400-114337200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:114326600-114335000	Weak transcription	Fetal Stomach	stomach
13	chr1:114326600-114335200	Weak transcription	HMEC	breast
14	chr1:114326600-114337800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:114326800-114335200	Weak transcription	HUVEC	blood vessel
16	chr1:114326800-114335800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:114326800-114335800	Weak transcription	NH-A	brain
18	chr1:114326800-114338600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:114326800-114340000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:114327000-114335000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:114327000-114335200	Weak transcription	NHDF-Ad	bronchial
22	chr1:114327000-114336000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:114327000-114337000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:114327200-114334800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:114327200-114337400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:114327400-114335000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:114327400-114335200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:114327400-114335400	Weak transcription	Fetal Brain Female	brain
29	chr1:114327400-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:114327400-114336400	Weak transcription	Thymus	Thymus
31	chr1:114327400-114336600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:114327400-114336800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:114327400-114337600	Weak transcription	Adipose Nuclei	Adipose
34	chr1:114327400-114337600	Weak transcription	Fetal Lung	lung
35	chr1:114327400-114339200	Weak transcription	HSMMtube	muscle
36	chr1:114327400-114341600	Weak transcription	Colonic Mucosa	Colon
37	chr1:114327400-114348800	Weak transcription	Spleen	Spleen
38	chr1:114327400-114351200	Weak transcription	Fetal Brain Male	brain
39	chr1:114327600-114335000	Weak transcription	Fetal Thymus	thymus
40	chr1:114327600-114335400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:114328000-114334800	Weak transcription	Primary B cells from cord blood	blood
42	chr1:114329200-114335000	Weak transcription	NHLF	lung
43	chr1:114329200-114335200	Weak transcription	Psoas Muscle	Psoas
44	chr1:114329200-114336000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:114329200-114336600	Weak transcription	Fetal Heart	heart
46	chr1:114329200-114337000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:114329200-114337200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:114329200-114339400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:114329200-114339600	Weak transcription	A549	lung
50	chr1:114329200-114340200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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