Variant report

Variant	rs1465638
Chromosome Location	chr2:10141191-10141192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10141011..10144036-chr2:10144143..10145916,3	K562	blood:
2	chr2:10140658..10143319-chr2:10184000..10185868,2	MCF-7	breast:
3	chr2:10134738..10137114-chr2:10139219..10141923,2	K562	blood:

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction
ENSG00000172059	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10179034	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10203214	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10203322	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1052835	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1052838	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11246	1.00[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470881	0.82[JPT][hapmap]
rs13385356	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13394227	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1594398	0.94[ASN][1000 genomes]
rs1594399	0.96[ASN][1000 genomes]
rs16867274	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16867280	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864537	0.96[ASN][1000 genomes]
rs1864538	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2099204	0.85[AMR][1000 genomes]
rs2163338	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791749	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3791750	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3791753	0.83[JPT][hapmap]
rs4668661	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4669515	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4669516	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6705493	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs6720380	0.84[AMR][1000 genomes]
rs6720387	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs6733635	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs6751681	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596286	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs930137	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs934303	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS 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	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1465638	KLF11	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:10113400-10141200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:10115000-10148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:10124800-10143200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:10124800-10149400	Weak transcription	Brain Anterior Caudate	brain
6	chr2:10125000-10147600	Weak transcription	K562	blood
7	chr2:10125000-10149400	Weak transcription	Psoas Muscle	Psoas
8	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:10126000-10144000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:10126400-10141200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:10128000-10142800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:10128000-10146400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:10130000-10142000	Strong transcription	HepG2	liver
14	chr2:10131600-10141200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:10131600-10149600	Weak transcription	Brain Substantia Nigra	brain
16	chr2:10132200-10145200	Weak transcription	Fetal Intestine Large	intestine
17	chr2:10132200-10146800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:10132400-10146400	Weak transcription	Left Ventricle	heart
19	chr2:10132400-10146800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:10133200-10146400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:10133400-10144200	Strong transcription	Esophagus	oesophagus
22	chr2:10134000-10145600	Weak transcription	Fetal Kidney	kidney
23	chr2:10134000-10145800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:10134200-10142000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:10134200-10147000	Weak transcription	HSMMtube	muscle
26	chr2:10134400-10144000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:10134800-10150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:10135400-10146400	Weak transcription	HUVEC	blood vessel
29	chr2:10136000-10144600	Weak transcription	Spleen	Spleen
30	chr2:10137000-10141400	Strong transcription	Fetal Intestine Small	intestine
31	chr2:10137000-10148000	Weak transcription	Hela-S3	cervix
32	chr2:10137200-10142200	Weak transcription	Dnd41	blood
33	chr2:10137200-10144600	Weak transcription	Brain Angular Gyrus	brain
34	chr2:10137200-10146200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:10137600-10142400	Weak transcription	Adipose Nuclei	Adipose
36	chr2:10137600-10142800	Weak transcription	NHDF-Ad	bronchial
37	chr2:10137600-10143400	Strong transcription	Placenta	Placenta
38	chr2:10137600-10146400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:10137600-10146600	Weak transcription	Fetal Heart	heart
40	chr2:10137600-10146800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:10137600-10149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:10137800-10146400	Weak transcription	Fetal Brain Female	brain
43	chr2:10138000-10141600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:10138400-10141600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:10138400-10143000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:10138800-10142000	Strong transcription	Liver	Liver
47	chr2:10139400-10143000	Weak transcription	Pancreas	Pancrea
48	chr2:10139600-10141400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:10139600-10143000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:10139600-10147000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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