Variant report

Variant	rs28406181
Chromosome Location	chr9:71467103-71467104
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	chr9:71320265..71322266-chr9:71464991..71467185,2	K562	blood:
2	chr9:71465582..71467985-chr9:71469828..71471360,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107242	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10114785	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10117789	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119445	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10121974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10124098	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11143755	1.00[EUR][1000 genomes]
rs11143975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143976	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143977	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144008	0.94[AFR][1000 genomes]
rs12336702	0.86[EUR][1000 genomes]
rs12336788	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12336829	0.82[ASN][1000 genomes]
rs12337137	0.81[AMR][1000 genomes]
rs12338217	0.81[AMR][1000 genomes]
rs12341382	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341508	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341625	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350205	0.81[AMR][1000 genomes]
rs12352746	0.84[AMR][1000 genomes]
rs1414945	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027023	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2039624	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28375745	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28444745	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3750375	0.81[AMR][1000 genomes]
rs3750376	0.81[AMR][1000 genomes]
rs3829061	0.81[AMR][1000 genomes]
rs56994943	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58984094	1.00[EUR][1000 genomes]
rs61453631	0.86[EUR][1000 genomes]
rs61547334	0.81[AMR][1000 genomes]
rs6560418	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7018854	0.81[ASN][1000 genomes]
rs7021259	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7024959	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7027620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7035068	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7037674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7041194	0.81[AMR][1000 genomes]
rs7046642	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048275	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73646761	1.00[EUR][1000 genomes]
rs7847379	0.81[AMR][1000 genomes]
rs7849727	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7851905	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7852244	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7855274	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7859396	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7863960	0.81[AMR][1000 genomes]
rs7865800	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869689	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7870383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953036	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv6548	chr9:71429527-71470917	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71438000-71491200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:71441000-71478600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:71448200-71485600	Weak transcription	Stomach Mucosa	stomach
4	chr9:71459000-71519200	Weak transcription	Colonic Mucosa	Colon
5	chr9:71459400-71480000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:71459800-71478600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr9:71460400-71495600	Weak transcription	Aorta	Aorta
8	chr9:71460600-71473800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr9:71460800-71517000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr9:71463400-71492800	Weak transcription	GM12878-XiMat	blood
11	chr9:71463600-71501800	Weak transcription	Small Intestine	intestine
12	chr9:71464200-71470800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:71465200-71467400	Enhancers	Brain Germinal Matrix	brain
14	chr9:71465600-71471200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:71465800-71467800	Enhancers	Fetal Heart	heart
16	chr9:71465800-71480200	Weak transcription	HepG2	liver
17	chr9:71466200-71467600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:71466400-71469400	Strong transcription	Fetal Intestine Small	intestine
19	chr9:71466800-71467400	Weak transcription	Left Ventricle	heart
20	chr9:71466800-71467400	Weak transcription	Pancreas	Pancrea
21	chr9:71466800-71467400	Weak transcription	K562	blood
22	chr9:71466800-71468400	Weak transcription	Gastric	stomach
23	chr9:71466800-71469200	Weak transcription	Primary B cells from cord blood	blood
24	chr9:71466800-71471200	Weak transcription	Right Atrium	heart
25	chr9:71466800-71478800	Weak transcription	Fetal Intestine Large	intestine

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