Variant report

Variant	rs6425257
Chromosome Location	chr1:173722980-173722981
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173720884..173724693-chr1:173791444..173794240,3	K562	blood:

Variant related genes	Relation type
ENSG00000117593	Chromatin interaction
ENSG00000120334	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10081990	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158663	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10399912	0.84[YRI][hapmap]
rs10798298	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912677	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912678	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912680	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912682	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912684	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1115487	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11487392	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12065033	1.00[EUR][1000 genomes]
rs12067571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070556	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073601	1.00[EUR][1000 genomes]
rs12074150	1.00[EUR][1000 genomes]
rs12080389	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082206	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12083423	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085748	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12085894	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094130	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095090	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12096832	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12098124	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322771	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1322772	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13375555	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1474907	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846383	0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846395	0.82[YRI][hapmap]
rs16846398	0.86[YRI][hapmap]
rs16846420	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2224657	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28578576	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs56124923	0.88[AMR][1000 genomes]
rs59845733	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6425256	0.82[YRI][hapmap]
rs6658217	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6663880	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6670574	1.00[EUR][1000 genomes]
rs6675762	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6686455	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6689764	1.00[AMR][1000 genomes]
rs6691327	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6691922	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6692452	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6695782	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6698348	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6702485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518130	0.93[YRI][hapmap];0.94[AMR][1000 genomes]
rs7522788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7534521	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7536773	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7544583	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550036	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7552840	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9282959	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9282960	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9286886	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9286887	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9286890	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9286894	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425413	0.84[YRI][hapmap]
rs9425414	0.82[YRI][hapmap]
rs9425415	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425418	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425419	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425420	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425421	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425422	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425423	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425424	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425425	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425426	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425734	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425736	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425738	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425740	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425741	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425742	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425746	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425747	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425750	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425751	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425752	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425758	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425759	0.93[YRI][hapmap];0.94[AMR][1000 genomes]
rs9425761	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425774	0.83[AMR][1000 genomes]
rs9442660	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9970488	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9970633	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv3598	chr1:173693027-173738687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173685200-173724600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:173685400-173725000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:173685800-173724800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:173686800-173725400	Weak transcription	Right Ventricle	heart
5	chr1:173694600-173724800	Weak transcription	HMEC	breast
6	chr1:173695400-173726000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:173695800-173725000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:173695800-173726000	Weak transcription	Esophagus	oesophagus
9	chr1:173695800-173729800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:173696200-173726000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:173696600-173723000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:173698000-173724800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:173699600-173725800	Weak transcription	Fetal Kidney	kidney
14	chr1:173703400-173725000	Weak transcription	Colonic Mucosa	Colon
15	chr1:173703400-173725000	Weak transcription	Psoas Muscle	Psoas
16	chr1:173703400-173726000	Weak transcription	Aorta	Aorta
17	chr1:173703400-173726000	Weak transcription	Spleen	Spleen
18	chr1:173703400-173726000	Weak transcription	NHEK	skin
19	chr1:173703600-173724400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:173703600-173724400	Weak transcription	GM12878-XiMat	blood
21	chr1:173703600-173724400	Weak transcription	HSMMtube	muscle
22	chr1:173703600-173724800	Weak transcription	Pancreas	Pancrea
23	chr1:173703800-173728200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:173704200-173725000	Weak transcription	NHLF	lung
25	chr1:173704400-173724400	Weak transcription	Gastric	stomach
26	chr1:173704400-173725000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:173704400-173725200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:173705000-173723600	Weak transcription	Lung	lung
29	chr1:173705400-173724800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:173705600-173724800	Weak transcription	Brain Angular Gyrus	brain
31	chr1:173705800-173725400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:173710200-173726000	Weak transcription	Brain Germinal Matrix	brain
33	chr1:173711600-173724800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:173711800-173724000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:173713400-173731600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:173718600-173725000	Weak transcription	NHDF-Ad	bronchial
37	chr1:173718800-173725800	Weak transcription	A549	lung
38	chr1:173719200-173724800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:173720000-173724800	Weak transcription	Fetal Brain Male	brain
40	chr1:173720000-173730000	Strong transcription	Primary B cells from cord blood	blood
41	chr1:173720000-173730600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:173720200-173727400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:173720200-173728000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:173720200-173729000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:173720200-173729000	Strong transcription	Dnd41	blood
46	chr1:173720200-173729600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:173720200-173729800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:173720200-173730000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:173720200-173730200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:173720400-173723000	Weak transcription	Right Atrium	heart

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