Variant report

Variant	rs13239106
Chromosome Location	chr7:40020954-40020955
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	chr7:39988014..39992779-chr7:40016991..40021232,5	K562	blood:

Variant related genes	Relation type
ENSG00000259826	Chromatin interaction
ENSG00000065883	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10046564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10224206	0.95[EUR][1000 genomes]
rs10225492	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10228596	1.00[CHB][hapmap]
rs10234693	0.82[CEU][hapmap]
rs10235989	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239324	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246466	0.81[CEU][hapmap]
rs10247292	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253590	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272514	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272641	0.81[CEU][hapmap]
rs10275761	0.82[CEU][hapmap]
rs10277422	1.00[CHB][hapmap]
rs10277853	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10279016	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082023	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1257699	0.82[CEU][hapmap]
rs12701787	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231977	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241453	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310480	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17434388	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs17435812	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496226	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496247	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526699	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052097	0.81[CEU][hapmap]
rs2140254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492942	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28547436	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638437	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34326687	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470312	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748607	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35052806	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35082351	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35226291	0.80[EUR][1000 genomes]
rs35618050	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273753	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4428576	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481477	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498451	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947071	0.82[EUR][1000 genomes]
rs73127832	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73127862	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731847	0.82[CEU][hapmap]
rs773382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773393	0.81[CEU][hapmap]
rs773402	0.82[CEU][hapmap]
rs773424	0.81[CEU][hapmap]
rs7780996	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794792	0.81[EUR][1000 genomes]
rs7797041	0.81[CEU][hapmap]
rs7799846	0.81[CEU][hapmap]
rs7811585	0.81[EUR][1000 genomes]
rs809558	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs878785	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9639817	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9639820	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9655036	1.00[CHB][hapmap]
rs9655407	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690347	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9986996	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986997	0.86[AMR][1000 genomes];0.99[EUR][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	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1015322	chr7:40006195-40141195	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv2761319	chr7:40006195-40142139	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv464436	chr7:40018693-40133044	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv606706	chr7:40018693-40133044	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39993600-40048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:39994200-40027200	Weak transcription	HSMM	muscle
3	chr7:39995200-40042600	Weak transcription	K562	blood
4	chr7:39997800-40027400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:39998000-40027200	Weak transcription	Hela-S3	cervix
6	chr7:40005600-40021000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr7:40005600-40021000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr7:40006800-40031200	Weak transcription	Fetal Stomach	stomach
9	chr7:40007200-40027200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:40007600-40027200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:40009400-40027200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:40009400-40027400	Weak transcription	Osteobl	bone
13	chr7:40009600-40027400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:40009800-40027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:40010000-40024600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:40010000-40026800	Weak transcription	NHEK	skin
17	chr7:40010200-40025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:40010400-40027200	Weak transcription	Esophagus	oesophagus
19	chr7:40011000-40021000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr7:40011200-40023600	Weak transcription	Lung	lung
21	chr7:40011200-40025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:40011400-40027400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr7:40014200-40021200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:40014800-40021200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr7:40015000-40023600	Weak transcription	Fetal Intestine Small	intestine
26	chr7:40016000-40021000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:40016600-40021000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr7:40016800-40027200	Weak transcription	A549	lung
29	chr7:40017400-40027400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:40017600-40024400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr7:40017800-40026800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:40017800-40027400	Weak transcription	Liver	Liver
33	chr7:40018000-40025000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:40018000-40025200	Weak transcription	Small Intestine	intestine
35	chr7:40018400-40024600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:40018400-40024600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr7:40018400-40027200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:40018400-40027400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:40018600-40023200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:40018600-40023200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:40018600-40023400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr7:40018600-40023800	Weak transcription	Psoas Muscle	Psoas
43	chr7:40018600-40024400	Weak transcription	Right Ventricle	heart
44	chr7:40018600-40047800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:40018800-40021000	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr7:40018800-40023200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:40018800-40025200	Weak transcription	Adipose Nuclei	Adipose
48	chr7:40018800-40027400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:40019200-40023800	Weak transcription	Spleen	Spleen
50	chr7:40019200-40025000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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