Variant report

Variant	rs16977312
Chromosome Location	chr15:57508142-57508143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57508073..57512585-chr15:57540435..57543693,4	K562	blood:
2	chr15:57210007..57212139-chr15:57506855..57509389,2	K562	blood:
3	chr15:57507579..57509152-chr15:57511369..57513515,2	K562	blood:
4	chr15:57506333..57510182-chr15:57512015..57516171,5	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1045665	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10518898	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10518904	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12437713	0.95[YRI][hapmap]
rs12900589	0.95[YRI][hapmap]
rs12900874	0.90[YRI][hapmap]
rs16953323	0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977199	0.91[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977201	0.91[YRI][hapmap]
rs16977217	0.91[YRI][hapmap];0.80[AMR][1000 genomes]
rs16977218	0.91[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977232	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977235	0.95[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977242	0.95[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977244	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977245	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs16977253	0.95[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977272	0.95[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977276	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977280	0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977284	0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977297	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977308	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977315	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977329	1.00[EUR][1000 genomes]
rs16977330	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977333	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977341	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977352	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977353	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977354	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977372	0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17415738	0.95[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1867639	1.00[EUR][1000 genomes]
rs2169466	0.95[YRI][hapmap]
rs2593220	1.00[EUR][1000 genomes]
rs2615251	1.00[EUR][1000 genomes]
rs2733316	1.00[EUR][1000 genomes]
rs2733317	1.00[EUR][1000 genomes]
rs2733343	1.00[EUR][1000 genomes]
rs2733345	1.00[EUR][1000 genomes]
rs28454221	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34560099	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7183392	0.86[YRI][hapmap]
rs935327	1.00[EUR][1000 genomes]
rs935329	1.00[EUR][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	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
3	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
5	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
6	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:57491400-57510000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:57491400-57510000	Weak transcription	Psoas Muscle	Psoas
10	chr15:57491400-57510200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr15:57491400-57511200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:57491600-57515200	Weak transcription	GM12878-XiMat	blood
13	chr15:57492400-57511600	Weak transcription	Left Ventricle	heart
14	chr15:57494200-57508600	Weak transcription	Dnd41	blood
15	chr15:57496400-57510200	Weak transcription	Small Intestine	intestine
16	chr15:57501200-57524400	Weak transcription	Thymus	Thymus
17	chr15:57501600-57510200	Weak transcription	Primary B cells from cord blood	blood
18	chr15:57502400-57509600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:57503000-57510400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:57503400-57508600	Weak transcription	Primary T cells from cord blood	blood
21	chr15:57504200-57508200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:57504400-57510200	Enhancers	Brain Hippocampus Middle	brain
23	chr15:57504600-57510000	Enhancers	Brain Anterior Caudate	brain
24	chr15:57504800-57510200	Enhancers	Brain Substantia Nigra	brain
25	chr15:57505000-57509800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr15:57505000-57510000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:57505000-57510200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:57505200-57508200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:57505200-57508200	Enhancers	NHLF	lung
30	chr15:57505200-57510000	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:57505200-57511400	Enhancers	Fetal Lung	lung
32	chr15:57505400-57508400	Enhancers	HSMM	muscle
33	chr15:57505800-57508200	Enhancers	Osteobl	bone
34	chr15:57505800-57509800	Enhancers	NHDF-Ad	bronchial
35	chr15:57505800-57510000	Enhancers	Fetal Kidney	kidney
36	chr15:57506000-57509200	Enhancers	A549	lung
37	chr15:57506000-57511600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:57506200-57508200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:57506200-57508200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:57506200-57508600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:57506400-57508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:57506400-57508200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:57506400-57508400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr15:57506400-57510000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr15:57506400-57510000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:57506400-57510000	Weak transcription	Ovary	ovary
47	chr15:57506400-57510200	Enhancers	Brain Cingulate Gyrus	brain
48	chr15:57506400-57510400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:57506600-57508200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:57506600-57508200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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