Variant report

Variant	rs2109339
Chromosome Location	chr7:40106145-40106146
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:40105682..40108224-chr7:40109570..40112415,2	K562	blood:

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10156182	0.97[ASN][1000 genomes]
rs10233552	0.96[ASN][1000 genomes]
rs10234693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10246466	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1024680	0.96[ASN][1000 genomes]
rs10252631	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10254394	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10268288	0.85[ASN][1000 genomes]
rs10272641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10275761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10951624	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10951625	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11972983	0.98[ASN][1000 genomes]
rs11977756	0.81[CHB][hapmap]
rs11980745	0.93[ASN][1000 genomes]
rs11983287	0.96[ASN][1000 genomes]
rs12334141	0.89[ASN][1000 genomes]
rs12531761	0.96[ASN][1000 genomes]
rs12531774	0.91[ASN][1000 genomes]
rs12532714	0.81[CHB][hapmap]
rs12533272	0.96[ASN][1000 genomes]
rs12536190	0.97[ASN][1000 genomes]
rs12536349	0.84[ASN][1000 genomes]
rs12536726	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12537125	0.99[ASN][1000 genomes]
rs12537320	0.96[ASN][1000 genomes]
rs1257698	0.96[ASN][1000 genomes]
rs1257699	0.86[CHB][hapmap]
rs12666454	0.88[ASN][1000 genomes]
rs12669872	0.97[ASN][1000 genomes]
rs13233333	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs1403381	0.93[ASN][1000 genomes]
rs1568645	0.83[ASN][1000 genomes]
rs17171637	0.80[CHB][hapmap]
rs17171645	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17171646	0.96[ASN][1000 genomes]
rs17171649	0.81[YRI][hapmap]
rs17171658	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17496429	0.94[ASN][1000 genomes]
rs17496670	0.99[ASN][1000 genomes]
rs17496733	0.97[ASN][1000 genomes]
rs17538125	0.97[ASN][1000 genomes]
rs1874232	0.87[CEU][hapmap]
rs2015842	0.96[ASN][1000 genomes]
rs2052097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2077124	0.95[ASN][1000 genomes]
rs2159488	0.88[ASN][1000 genomes]
rs2159489	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2302341	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2329693	0.97[ASN][1000 genomes]
rs33999222	0.94[ASN][1000 genomes]
rs3800799	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3800802	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3801238	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3847019	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3847020	0.94[ASN][1000 genomes]
rs3847021	0.88[ASN][1000 genomes]
rs3911836	0.96[ASN][1000 genomes]
rs3911889	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4344004	0.80[CHB][hapmap]
rs4720347	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4720348	0.97[ASN][1000 genomes]
rs4720349	0.99[ASN][1000 genomes]
rs4720352	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4723925	0.91[ASN][1000 genomes]
rs4723927	0.96[ASN][1000 genomes]
rs4723928	0.96[ASN][1000 genomes]
rs4723929	0.86[ASN][1000 genomes]
rs6952597	0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs6960111	0.96[ASN][1000 genomes]
rs6965022	0.84[YRI][hapmap]
rs6966917	0.92[ASN][1000 genomes]
rs6975853	0.88[ASN][1000 genomes]
rs731847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs731848	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.97[ASN][1000 genomes]
rs73394665	0.88[ASN][1000 genomes]
rs758696	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs773393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs773397	0.89[ASN][1000 genomes]
rs773402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs773410	0.85[ASN][1000 genomes]
rs773411	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs773413	0.92[ASN][1000 genomes]
rs773424	0.85[CHB][hapmap]
rs7779663	0.97[ASN][1000 genomes]
rs7797041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7799846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7809754	0.81[YRI][hapmap]
rs9639818	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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
7	nsv606707	chr7:40021044-40133044	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv606708	chr7:40021044-40157040	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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
9	nsv887978	chr7:40030488-40124137	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv429748	chr7:40054760-40140660	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	esv2756801	chr7:40060180-40269583	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	esv2759525	chr7:40060180-40269583	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv887979	chr7:40067021-40193535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv887980	chr7:40067021-40203356	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv887981	chr7:40075461-40203356	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv971193	chr7:40075881-40197955	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	esv34547	chr7:40077032-40230965	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv824080	chr7:40077089-40198644	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	nsv464437	chr7:40094641-40197168	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
20	nsv606709	chr7:40094641-40197168	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
21	nsv1032278	chr7:40097371-40396300	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
22	nsv887982	chr7:40098787-40193535	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2109339	CDC2L5	cis	normal skin	skin_eQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40028000-40127800	Weak transcription	Colonic Mucosa	Colon
2	chr7:40043600-40127800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:40055600-40126400	Weak transcription	Aorta	Aorta
4	chr7:40055800-40110000	Weak transcription	Gastric	stomach
5	chr7:40055800-40127600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:40055800-40127600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:40056000-40112200	Weak transcription	HepG2	liver
8	chr7:40056200-40128600	Weak transcription	A549	lung
9	chr7:40058600-40126800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:40059000-40125200	Weak transcription	Fetal Kidney	kidney
11	chr7:40072000-40130400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr7:40076200-40106800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:40077200-40127800	Weak transcription	Esophagus	oesophagus
14	chr7:40080200-40132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:40082000-40127800	Weak transcription	Pancreas	Pancrea
16	chr7:40082600-40128200	Weak transcription	Spleen	Spleen
17	chr7:40083400-40127400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:40086400-40127800	Weak transcription	Thymus	Thymus
19	chr7:40092600-40127600	Weak transcription	Brain Substantia Nigra	brain
20	chr7:40093800-40127600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:40094800-40127800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr7:40095800-40127800	Weak transcription	Fetal Brain Female	brain
23	chr7:40096600-40126600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:40096800-40126600	Weak transcription	Lung	lung
25	chr7:40097200-40108400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:40097200-40127600	Weak transcription	HSMMtube	muscle
27	chr7:40097200-40132600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:40097200-40132600	Weak transcription	Right Ventricle	heart
29	chr7:40097400-40106600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:40097400-40108000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr7:40098200-40132400	Weak transcription	Psoas Muscle	Psoas
32	chr7:40098400-40119400	Weak transcription	Small Intestine	intestine
33	chr7:40098600-40110800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:40098600-40127600	Weak transcription	Brain Hippocampus Middle	brain
35	chr7:40099000-40108800	Weak transcription	Fetal Heart	heart
36	chr7:40099000-40111000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr7:40099000-40111400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:40099000-40119400	Weak transcription	Brain Anterior Caudate	brain
39	chr7:40099000-40126600	Weak transcription	Brain Angular Gyrus	brain
40	chr7:40099200-40123600	Weak transcription	Ovary	ovary
41	chr7:40099400-40118200	Weak transcription	Left Ventricle	heart
42	chr7:40099800-40132600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:40101000-40107200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:40101000-40109000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr7:40101200-40106400	Strong transcription	Liver	Liver
46	chr7:40101200-40108200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:40101400-40109200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:40101400-40109400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:40101600-40118600	Weak transcription	Brain Germinal Matrix	brain
50	chr7:40101800-40108000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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