Variant report

Variant	rs930137
Chromosome Location	chr2:10143901-10143902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10141011..10144036-chr2:10144143..10145916,3	K562	blood:
2	chr2:10141557..10144433-chr2:10145259..10147096,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYS1-3	chr2:10143286-10144213	ENSG00000188525.3

Variant related genes	Relation type
ENSG00000188525	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10179034	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10203214	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10203322	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052835	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1052838	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11246	0.84[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
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]
rs1465638	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]
rs1594398	0.93[ASN][1000 genomes]
rs1594399	0.95[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];0.96[ASN][1000 genomes]
rs1864537	0.95[ASN][1000 genomes]
rs1864538	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2099204	0.85[AMR][1000 genomes]
rs2163338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791749	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3791750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4669516	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6705493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs6720380	0.84[AMR][1000 genomes]
rs6720387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs6733635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs6751681	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596286	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs934303	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	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
2	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
3	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
4	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
5	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
rs930137	KLF11	cis	cerebellum	SCAN

Chromatin state (count:52 , 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	chr2:10115000-10148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:10124800-10149400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:10125000-10147600	Weak transcription	K562	blood
5	chr2:10125000-10149400	Weak transcription	Psoas Muscle	Psoas
6	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:10126000-10144000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:10128000-10146400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:10131600-10149600	Weak transcription	Brain Substantia Nigra	brain
10	chr2:10132200-10145200	Weak transcription	Fetal Intestine Large	intestine
11	chr2:10132200-10146800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:10132400-10146400	Weak transcription	Left Ventricle	heart
13	chr2:10132400-10146800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:10133200-10146400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:10133400-10144200	Strong transcription	Esophagus	oesophagus
16	chr2:10134000-10145600	Weak transcription	Fetal Kidney	kidney
17	chr2:10134000-10145800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:10134200-10147000	Weak transcription	HSMMtube	muscle
19	chr2:10134400-10144000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:10134800-10150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:10135400-10146400	Weak transcription	HUVEC	blood vessel
22	chr2:10136000-10144600	Weak transcription	Spleen	Spleen
23	chr2:10137000-10148000	Weak transcription	Hela-S3	cervix
24	chr2:10137200-10144600	Weak transcription	Brain Angular Gyrus	brain
25	chr2:10137200-10146200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:10137600-10146400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:10137600-10146600	Weak transcription	Fetal Heart	heart
28	chr2:10137600-10146800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:10137600-10149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:10137800-10146400	Weak transcription	Fetal Brain Female	brain
31	chr2:10139600-10147000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:10139800-10146400	Weak transcription	Gastric	stomach
33	chr2:10139800-10150400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:10141000-10144600	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:10141000-10147000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:10141400-10144000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:10141400-10145200	Weak transcription	Fetal Intestine Small	intestine
38	chr2:10141400-10146400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:10141400-10146800	Weak transcription	Lung	lung
40	chr2:10141600-10160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:10142000-10144800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:10142000-10146400	Weak transcription	Liver	Liver
43	chr2:10142000-10147600	Weak transcription	HepG2	liver
44	chr2:10142400-10148200	Enhancers	Adipose Nuclei	Adipose
45	chr2:10142600-10147000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:10142800-10145800	Enhancers	NHDF-Ad	bronchial
47	chr2:10142800-10148000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr2:10143000-10144200	Enhancers	Fetal Muscle Trunk	muscle
49	chr2:10143400-10144200	Genic enhancers	Placenta	Placenta
50	chr2:10143400-10144200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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