Variant report

Variant	rs589892
Chromosome Location	chr6:144613989-144613990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144613353..144615831-chr6:144616673..144618969,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs2473129	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2473153	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502621	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs583341	0.92[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs583788	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs584283	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs586016	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs586471	0.92[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs586553	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs587691	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs587889	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs590329	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs590362	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs591311	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs592388	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs592667	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs598222	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs599074	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs601816	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs601873	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs602764	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs603692	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs612928	0.92[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs615755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs616619	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs619750	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs623320	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs632972	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs633106	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs633802	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs643596	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs644124	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs646837	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs647282	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs649426	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs652262	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs652765	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs658562	0.93[EUR][1000 genomes]
rs659899	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs660286	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs660307	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs660770	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs662419	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs664541	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs664721	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs665135	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs667740	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs667765	0.92[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs672468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676859	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs680093	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs681854	0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs681916	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs682704	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74671	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs849661	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs589892	RP1-83M4.2	cis	Nerve Tibial	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144608400-144626600	Weak transcription	Spleen	Spleen
2	chr6:144608600-144616600	Weak transcription	Pancreas	Pancrea
3	chr6:144608600-144616800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:144608600-144617200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:144608600-144617200	Weak transcription	Gastric	stomach
6	chr6:144608600-144617800	Weak transcription	Stomach Mucosa	stomach
7	chr6:144608600-144619400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:144608600-144626800	Weak transcription	Esophagus	oesophagus
9	chr6:144608600-144629800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:144608600-144631400	Weak transcription	Colonic Mucosa	Colon
11	chr6:144608800-144616800	Weak transcription	Fetal Intestine Large	intestine
12	chr6:144608800-144617600	Weak transcription	Right Atrium	heart
13	chr6:144609000-144614000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:144609000-144616400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:144609000-144616800	Weak transcription	Aorta	Aorta
16	chr6:144609200-144614400	Weak transcription	NHEK	skin
17	chr6:144609200-144616000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:144609200-144616400	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:144609200-144616400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:144609200-144616600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:144609200-144616600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:144609200-144616600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:144609200-144616600	Weak transcription	Left Ventricle	heart
24	chr6:144609200-144616800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:144609200-144616800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:144609200-144616800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:144609200-144616800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:144609200-144616800	Weak transcription	Fetal Lung	lung
29	chr6:144609200-144616800	Weak transcription	Fetal Stomach	stomach
30	chr6:144609200-144617000	Weak transcription	Right Ventricle	heart
31	chr6:144609200-144617200	Weak transcription	Fetal Intestine Small	intestine
32	chr6:144609200-144617200	Weak transcription	Psoas Muscle	Psoas
33	chr6:144609200-144617800	Weak transcription	Brain Anterior Caudate	brain
34	chr6:144609200-144617800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:144609200-144618000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:144609200-144618000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:144609200-144618200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:144609200-144618600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:144609200-144623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:144609200-144623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:144609200-144626800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:144609200-144641600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:144609400-144614000	Weak transcription	A549	lung
44	chr6:144609400-144614600	Weak transcription	NH-A	brain
45	chr6:144609400-144616400	Weak transcription	Fetal Kidney	kidney
46	chr6:144609400-144616400	Weak transcription	Dnd41	blood
47	chr6:144609400-144616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:144609400-144616800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:144609400-144616800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:144609400-144617600	Weak transcription	Colon Smooth Muscle	Colon

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