Variant report

Variant	rs935329
Chromosome Location	chr15:57509961-57509962
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr15:57509892-57510350	HL-60	blood:	n/a	n/a
2	MXI1	chr15:57509838-57512067	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr15:57509895-57510364	SK-N-MC	brain:	n/a	n/a
4	SPI1	chr15:57509954-57510256	HL-60	blood:	n/a	n/a
5	MYC	chr15:57509961-57510271	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:57508073..57512585-chr15:57540435..57543693,4	K562	blood:
2	chr15:57463088..57465756-chr15:57508585..57510347,2	K562	blood:
3	chr15:57506333..57510182-chr15:57512015..57516171,5	K562	blood:

Variant related genes	Relation type
TCF12	TF binding region
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1045665	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs10518898	1.00[EUR][1000 genomes]
rs10518904	0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16953323	1.00[EUR][1000 genomes]
rs16977218	1.00[EUR][1000 genomes]
rs16977232	1.00[EUR][1000 genomes]
rs16977235	1.00[EUR][1000 genomes]
rs16977242	1.00[EUR][1000 genomes]
rs16977244	1.00[EUR][1000 genomes]
rs16977245	1.00[EUR][1000 genomes]
rs16977253	1.00[EUR][1000 genomes]
rs16977272	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16977276	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16977280	1.00[EUR][1000 genomes]
rs16977284	1.00[EUR][1000 genomes]
rs16977297	1.00[EUR][1000 genomes]
rs16977308	0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[EUR][1000 genomes]
rs16977312	1.00[EUR][1000 genomes]
rs16977315	1.00[EUR][1000 genomes]
rs16977329	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977330	1.00[EUR][1000 genomes]
rs16977333	1.00[EUR][1000 genomes]
rs16977341	1.00[EUR][1000 genomes]
rs16977352	1.00[EUR][1000 genomes]
rs16977353	0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[EUR][1000 genomes]
rs16977354	1.00[EUR][1000 genomes]
rs16977372	1.00[EUR][1000 genomes]
rs17415738	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs1867639	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1867641	1.00[YRI][hapmap]
rs2593217	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2593220	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2593221	0.85[ASW][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap]
rs2615251	1.00[EUR][1000 genomes]
rs2703599	0.96[YRI][hapmap]
rs2733304	0.83[AFR][1000 genomes]
rs2733316	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2733317	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2733323	0.96[YRI][hapmap]
rs2733343	0.96[YRI][hapmap];1.00[EUR][1000 genomes]
rs2733345	0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28454221	1.00[EUR][1000 genomes]
rs34560099	1.00[EUR][1000 genomes]
rs7180558	0.96[YRI][hapmap]
rs8037987	0.96[YRI][hapmap]
rs8042322	0.96[YRI][hapmap]
rs8043103	0.96[YRI][hapmap]
rs935327	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs997683	0.96[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	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:96 , 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	chr15:57496400-57510200	Weak transcription	Small Intestine	intestine
15	chr15:57501200-57524400	Weak transcription	Thymus	Thymus
16	chr15:57501600-57510200	Weak transcription	Primary B cells from cord blood	blood
17	chr15:57503000-57510400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:57504400-57510200	Enhancers	Brain Hippocampus Middle	brain
19	chr15:57504600-57510000	Enhancers	Brain Anterior Caudate	brain
20	chr15:57504800-57510200	Enhancers	Brain Substantia Nigra	brain
21	chr15:57505000-57510000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:57505000-57510200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:57505200-57510000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:57505200-57511400	Enhancers	Fetal Lung	lung
25	chr15:57505800-57510000	Enhancers	Fetal Kidney	kidney
26	chr15:57506000-57511600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:57506400-57510000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr15:57506400-57510000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:57506400-57510000	Weak transcription	Ovary	ovary
30	chr15:57506400-57510200	Enhancers	Brain Cingulate Gyrus	brain
31	chr15:57506400-57510400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:57506600-57510000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:57506600-57510400	Weak transcription	Fetal Intestine Large	intestine
34	chr15:57506600-57511000	Weak transcription	Fetal Intestine Small	intestine
35	chr15:57506800-57511400	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr15:57507000-57519800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:57507200-57510000	Weak transcription	Liver	Liver
38	chr15:57507200-57510000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:57507400-57510000	Enhancers	Adipose Nuclei	Adipose
40	chr15:57507400-57510000	Enhancers	HSMMtube	muscle
41	chr15:57507400-57510200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:57507400-57511200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:57507400-57511800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr15:57507600-57511000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr15:57508000-57511200	Enhancers	Stomach Mucosa	stomach
46	chr15:57508200-57522800	Weak transcription	Fetal Thymus	thymus
47	chr15:57508600-57510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:57508600-57510000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:57508600-57510000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr15:57508600-57510000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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