Variant report

Variant	rs589238
Chromosome Location	chr6:161423049-161423050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161422502..161428879-chr6:161429746..161435781,7	K562	blood:
2	chr6:161421006..161425101-chr6:161625177..161629259,4	K562	blood:
3	chr6:161421302..161424014-chr6:161424627..161426475,2	K562	blood:
4	chr6:161422584..161426203-chr6:161439783..161443132,3	K562	blood:
5	chr6:161411515..161414164-chr6:161420734..161423757,3	MCF-7	breast:
6	chr6:161421443..161424452-chr6:161554706..161556451,3	K562	blood:

Variant related genes	Relation type
ENSG00000272841	Chromatin interaction
ENSG00000085511	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12174748	0.93[EUR][1000 genomes]
rs12203648	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs12665456	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13200744	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13206391	0.93[EUR][1000 genomes]
rs13209847	0.97[EUR][1000 genomes]
rs1562027	0.83[CHB][hapmap]
rs35894036	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734461	0.89[CHB][hapmap]
rs3736569	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3778219	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs3798907	0.97[EUR][1000 genomes]
rs3798910	0.93[EUR][1000 genomes]
rs3798912	0.97[EUR][1000 genomes]
rs3798913	0.97[EUR][1000 genomes]
rs4709485	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs588284	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590988	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs593184	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs594555	0.87[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs594602	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs619831	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs628075	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629015	0.94[ASN][1000 genomes]
rs630006	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs630430	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs643706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644110	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs645406	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs655382	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs657616	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs671335	0.87[ASN][1000 genomes]
rs674220	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675538	0.96[ASN][1000 genomes]
rs685939	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686392	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686755	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901173	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs6901968	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs6913867	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs71565787	0.83[EUR][1000 genomes]
rs71565788	0.93[EUR][1000 genomes]
rs7756711	0.94[CHB][hapmap]
rs787784	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796835	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295134	0.83[CHB][hapmap]
rs9347478	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs9355327	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs9355861	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9364587	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9365235	1.00[CEU][hapmap]
rs9365249	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9365251	0.93[EUR][1000 genomes]
rs9458102	0.82[CHB][hapmap]
rs9458114	0.80[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	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161413800-161432000	Weak transcription	Aorta	Aorta
2	chr6:161413800-161433000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:161414000-161430800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:161414000-161432000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:161414200-161431600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:161414200-161431600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:161414200-161458200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:161414400-161469600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:161414600-161432800	Weak transcription	Fetal Stomach	stomach
10	chr6:161414600-161442600	Weak transcription	Primary B cells from cord blood	blood
11	chr6:161414600-161457400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:161415600-161427800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:161415600-161450000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:161416600-161475200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:161416800-161436200	Weak transcription	Fetal Intestine Small	intestine
16	chr6:161417400-161449000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:161417600-161430200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:161417800-161433600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:161418000-161424400	Weak transcription	Pancreas	Pancrea
20	chr6:161418000-161424400	Weak transcription	Osteobl	bone
21	chr6:161418000-161432000	Weak transcription	Small Intestine	intestine
22	chr6:161418000-161432800	Weak transcription	Esophagus	oesophagus
23	chr6:161418000-161432800	Weak transcription	Right Atrium	heart
24	chr6:161418000-161434800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:161418000-161448800	Weak transcription	Lung	lung
26	chr6:161418400-161430800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:161418800-161432400	Weak transcription	Ovary	ovary
28	chr6:161419000-161427600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:161420000-161434800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:161420800-161423200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:161420800-161431800	Weak transcription	Fetal Lung	lung
32	chr6:161421600-161423800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:161422400-161423200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr6:161422400-161423200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:161422400-161423200	Enhancers	Brain Germinal Matrix	brain
36	chr6:161422400-161423400	Enhancers	Colon Smooth Muscle	Colon
37	chr6:161422400-161423400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:161422400-161423600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr6:161422800-161423200	Enhancers	Liver	Liver
40	chr6:161422800-161423400	Enhancers	Fetal Heart	heart
41	chr6:161422800-161428000	Weak transcription	Left Ventricle	heart
42	chr6:161422800-161428000	Weak transcription	Psoas Muscle	Psoas
43	chr6:161422800-161428400	Weak transcription	GM12878-XiMat	blood
44	chr6:161422800-161431200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:161422800-161431200	Weak transcription	HMEC	breast
46	chr6:161422800-161432000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:161422800-161433600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:161422800-161434600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:161422800-161441000	Weak transcription	K562	blood
50	chr6:161423000-161423200	Active TSS	Pancreatic Islets	Pancreatic Islet

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