Variant report

Variant	rs648412
Chromosome Location	chr11:57516602-57516603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57516134-57516602	K562	blood:	n/a	n/a
2	POLR2A	chr11:57516428-57516647	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57513714..57516909-chr11:57568303..57570046,3	K562	blood:
2	chr11:57514253..57516697-chr11:57521037..57524860,3	K562	blood:
3	chr11:57507833..57511012-chr11:57515890..57519512,4	MCF-7	breast:
4	chr11:57515725..57517383-chr11:57527700..57530343,2	MCF-7	breast:

Variant related genes	Relation type
CTNND1	TF binding region
ENSG00000198561	Chromatin interaction
ENSG00000211450	Chromatin interaction
ENSG00000254732	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10444364	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10736687	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10750868	1.00[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10896643	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12284427	1.00[AMR][1000 genomes]
rs1313360	1.00[ASN][1000 genomes]
rs1553827	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1798174	1.00[ASN][1000 genomes]
rs1939322	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2860261	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34430954	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs474073	1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs474464	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs505995	1.00[ASN][1000 genomes]
rs523739	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs529838	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap]
rs542777	1.00[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs552122	1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs554140	1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs557051	1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55786036	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55838210	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56879142	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57759830	1.00[ASN][1000 genomes]
rs58176671	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs585190	1.00[ASN][1000 genomes]
rs58851976	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59046396	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60076210	1.00[ASN][1000 genomes]
rs60282001	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60897155	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61444907	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61638601	1.00[ASN][1000 genomes]
rs61743110	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs627861	1.00[ASN][1000 genomes]
rs635663	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs637116	0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7103407	1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7103768	1.00[ASN][1000 genomes]
rs7110490	1.00[ASN][1000 genomes]
rs7112557	1.00[ASN][1000 genomes]
rs7118249	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7118308	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7122105	0.87[AMR][1000 genomes]
rs7131175	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73472468	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73474417	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73474449	1.00[ASN][1000 genomes]
rs73474453	1.00[ASN][1000 genomes]
rs73474454	1.00[ASN][1000 genomes]
rs73474455	1.00[ASN][1000 genomes]
rs73482748	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482786	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482796	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482801	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7928666	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7938752	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs947940	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57509800-57519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57510200-57518400	Weak transcription	Psoas Muscle	Psoas
3	chr11:57510400-57519000	Weak transcription	Stomach Mucosa	stomach
4	chr11:57510400-57519400	Weak transcription	Right Atrium	heart
5	chr11:57510400-57519400	Weak transcription	Small Intestine	intestine
6	chr11:57510400-57528800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:57510600-57517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:57511800-57519400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:57511800-57528800	Weak transcription	Fetal Brain Male	brain
10	chr11:57512000-57528800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:57512200-57528800	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:57512400-57519000	Weak transcription	HepG2	liver
13	chr11:57512400-57519400	Weak transcription	HUVEC	blood vessel
14	chr11:57512400-57520800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:57512400-57528800	Weak transcription	HSMM	muscle
16	chr11:57512600-57518600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:57512600-57519000	Weak transcription	A549	lung
18	chr11:57512600-57519400	Weak transcription	Ovary	ovary
19	chr11:57512600-57519400	Weak transcription	Pancreas	Pancrea
20	chr11:57512600-57519400	Weak transcription	HMEC	breast
21	chr11:57512600-57521800	Weak transcription	Fetal Lung	lung
22	chr11:57512600-57526400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:57512600-57528800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:57512800-57518000	Weak transcription	K562	blood
25	chr11:57512800-57521600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:57512800-57528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:57513000-57518600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr11:57513000-57528800	Weak transcription	HSMMtube	muscle
29	chr11:57513200-57519400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:57513200-57528600	Weak transcription	NHEK	skin
31	chr11:57513400-57516800	Weak transcription	Esophagus	oesophagus
32	chr11:57513600-57517000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:57513600-57518200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:57513600-57519000	Weak transcription	NHLF	lung
35	chr11:57513600-57519200	Weak transcription	Brain Substantia Nigra	brain
36	chr11:57513600-57519400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr11:57513600-57519400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr11:57513600-57519400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr11:57513600-57519400	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:57513600-57519400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:57513600-57519400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr11:57513600-57520200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:57513600-57520200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr11:57513600-57528800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr11:57513600-57528800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr11:57513600-57528800	Weak transcription	Colonic Mucosa	Colon
47	chr11:57513600-57529200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:57513600-57531200	Weak transcription	Gastric	stomach
49	chr11:57513800-57516800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr11:57513800-57518600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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