Variant report

Variant	rs7599990
Chromosome Location	chr2:39255676-39255677
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	chr2:39245988..39251682-chr2:39252776..39257874,7	K562	blood:
2	chr2:39247780..39252503-chr2:39254556..39258149,5	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10184046	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10184855	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10186842	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10188701	1.00[EUR][1000 genomes]
rs10189440	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10194533	1.00[EUR][1000 genomes]
rs10196863	1.00[EUR][1000 genomes]
rs10199955	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10202876	1.00[EUR][1000 genomes]
rs10203565	1.00[EUR][1000 genomes]
rs10207187	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10207984	1.00[EUR][1000 genomes]
rs10495882	1.00[EUR][1000 genomes]
rs10495883	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12329307	1.00[EUR][1000 genomes]
rs13387231	1.00[EUR][1000 genomes]
rs13394446	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13407659	1.00[EUR][1000 genomes]
rs13411756	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13416725	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13424493	1.00[EUR][1000 genomes]
rs13425165	1.00[EUR][1000 genomes]
rs13428418	1.00[EUR][1000 genomes]
rs13432395	1.00[EUR][1000 genomes]
rs1451278	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023148	1.00[EUR][1000 genomes]
rs17023149	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023214	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023241	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17023272	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17023292	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1901290	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2218850	1.00[EUR][1000 genomes]
rs2373466	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373472	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099938	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099947	1.00[CEU][hapmap]
rs3099953	1.00[EUR][1000 genomes]
rs3099973	1.00[EUR][1000 genomes]
rs3099986	1.00[EUR][1000 genomes]
rs3099996	1.00[EUR][1000 genomes]
rs3099997	1.00[EUR][1000 genomes]
rs3112145	1.00[EUR][1000 genomes]
rs3112146	1.00[EUR][1000 genomes]
rs3112148	1.00[EUR][1000 genomes]
rs3112155	1.00[EUR][1000 genomes]
rs3112157	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112158	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112160	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112164	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112174	1.00[EUR][1000 genomes]
rs3112176	1.00[CEU][hapmap]
rs3112177	1.00[EUR][1000 genomes]
rs41280639	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55890805	1.00[EUR][1000 genomes]
rs56269328	1.00[EUR][1000 genomes]
rs56724744	1.00[EUR][1000 genomes]
rs57359008	1.00[EUR][1000 genomes]
rs59259697	1.00[EUR][1000 genomes]
rs59988245	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs61049772	0.81[ASN][1000 genomes]
rs61521176	0.86[ASN][1000 genomes]
rs61596046	1.00[EUR][1000 genomes]
rs6544200	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6709646	0.86[ASN][1000 genomes]
rs6729359	0.86[ASN][1000 genomes]
rs6734212	1.00[EUR][1000 genomes]
rs6737680	1.00[EUR][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6754613	1.00[EUR][1000 genomes]
rs718312	1.00[EUR][1000 genomes]
rs72906436	1.00[EUR][1000 genomes]
rs72906467	1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs72918721	0.86[ASN][1000 genomes]
rs72925431	1.00[EUR][1000 genomes]
rs72925433	1.00[EUR][1000 genomes]
rs72925439	1.00[EUR][1000 genomes]
rs7340303	1.00[EUR][1000 genomes]
rs73930506	1.00[EUR][1000 genomes]
rs7559174	0.82[JPT][hapmap]
rs7559586	1.00[EUR][1000 genomes]
rs7564481	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7565814	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7571608	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7571719	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7574214	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7583010	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7589303	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9646968	1.00[EUR][1000 genomes]
rs9678084	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]

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	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	36 gene(s)	inside rSNPs	diseases
4	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
2	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
3	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
5	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39235600-39259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:39235600-39259800	Weak transcription	Spleen	Spleen
10	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
11	chr2:39235600-39295800	Weak transcription	NHLF	lung
12	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
13	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
14	chr2:39235800-39257800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:39236000-39260000	Weak transcription	Hela-S3	cervix
18	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
19	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:39236000-39305600	Weak transcription	Gastric	stomach
21	chr2:39236200-39305600	Weak transcription	Lung	lung
22	chr2:39236400-39263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:39237000-39260200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:39237600-39257600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:39238400-39256400	Weak transcription	Fetal Intestine Small	intestine
26	chr2:39238400-39260600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:39238600-39256400	Weak transcription	Fetal Stomach	stomach
28	chr2:39240800-39257600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:39240800-39257800	Weak transcription	Fetal Brain Female	brain
30	chr2:39240800-39262600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:39241200-39256600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:39241200-39259800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:39241600-39276400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:39241600-39292800	Weak transcription	GM12878-XiMat	blood
36	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
37	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:39244800-39257800	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:39246200-39259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:39246600-39274000	Weak transcription	Fetal Kidney	kidney
41	chr2:39246800-39257800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:39248000-39257600	Weak transcription	Left Ventricle	heart
43	chr2:39248000-39257800	Weak transcription	HSMMtube	muscle
44	chr2:39249600-39262000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:39250000-39282200	Weak transcription	Brain Anterior Caudate	brain
46	chr2:39250000-39292800	Weak transcription	Psoas Muscle	Psoas
47	chr2:39250200-39256400	Weak transcription	Thymus	Thymus
48	chr2:39250200-39256600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:39250200-39259600	Weak transcription	Osteobl	bone
50	chr2:39250200-39295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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