Variant report

Variant	rs478475
Chromosome Location	chr11:77131300-77131301
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	chr11:76954546..76956343-chr11:77129983..77132787,2	K562	blood:
2	chr11:77121279..77124216-chr11:77128750..77132079,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149269	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10793248	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11607378	0.83[EUR][1000 genomes]
rs1225479	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1840151	0.82[ASN][1000 genomes]
rs2007466	0.82[EUR][1000 genomes]
rs2602458	0.80[ASN][1000 genomes]
rs2725812	0.92[EUR][1000 genomes]
rs2725830	0.80[ASN][1000 genomes]
rs2853097	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3015984	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015989	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015991	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015993	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3019240	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019243	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3019258	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34420077	0.84[EUR][1000 genomes]
rs4433591	0.84[EUR][1000 genomes]
rs473012	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs476925	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs478134	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482243	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs487322	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs489038	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs491781	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs492527	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4944153	0.80[EUR][1000 genomes]
rs4944155	0.83[EUR][1000 genomes]
rs4944158	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4945162	0.82[EUR][1000 genomes]
rs4945166	0.83[EUR][1000 genomes]
rs4945169	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs495889	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497172	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs497946	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs499880	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs500731	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs514191	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs517511	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs538670	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs539906	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs556696	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs561153	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs562939	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs568309	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57129983	0.83[EUR][1000 genomes]
rs575662	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs576079	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs576997	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs584909	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs599437	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs605910	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs614775	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs618012	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61901769	0.82[EUR][1000 genomes]
rs61901771	0.80[EUR][1000 genomes]
rs61901802	0.89[EUR][1000 genomes]
rs628325	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs635291	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639857	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6592715	0.85[EUR][1000 genomes]
rs667331	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs683497	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs688212	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7118869	0.89[EUR][1000 genomes]
rs721382	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73496890	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928731	0.83[EUR][1000 genomes]
rs98703	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised 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	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77123000-77131400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:77123400-77131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:77123400-77147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:77123400-77147200	Weak transcription	Pancreas	Pancrea
5	chr11:77123600-77132600	Weak transcription	Stomach Mucosa	stomach
6	chr11:77123600-77135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:77123600-77135800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:77124000-77135000	Weak transcription	Brain Anterior Caudate	brain
9	chr11:77124200-77147000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:77124600-77133400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:77128400-77132400	Enhancers	Fetal Intestine Large	intestine
12	chr11:77128800-77132400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr11:77129200-77133000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr11:77129400-77133000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr11:77129400-77133000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr11:77129400-77133000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr11:77129400-77133400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr11:77129800-77131400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:77130000-77133200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:77130000-77139000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr11:77130000-77147000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:77130200-77131400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:77130200-77131600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:77130200-77135200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:77130200-77143000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:77130400-77131400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:77130400-77131800	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr11:77130600-77138000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:77130800-77132000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:77131000-77131800	Enhancers	GM12878-XiMat	blood
31	chr11:77131000-77132200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr11:77131000-77135200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:77131200-77131400	Enhancers	Fetal Intestine Small	intestine
34	chr11:77131200-77131800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:77131200-77132800	Enhancers	H1 Cell Line	embryonic stem cell

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