Variant report

Variant	nsv945439
Chromosome Location	chr1:247362491-247364849
allele	n/a
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	CTCF	chr1:247362360-247362510	GM12872	blood:	n/a	n/a
2	CTCF	chr1:247362460-247362610	HCT-116	colon:	n/a	n/a
3	POLR2A	chr1:247362519-247362580	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247336789..247339124-chr1:247364118..247365695,2	K562	blood:
2	chr1:247361273..247363730-chr1:247370221..247373518,3	K562	blood:

Variant related genes	Relation type
MIR3916	TF binding region
ENSG00000227671	chromatin interactions
ENSG00000224014	chromatin interactions

Extended variants
information (count: 88 )
Associated
traits (count: 30 )

Variant overlapped rSNPs/rCNVs (count:88 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543285311	chr1:247362580-247362581	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs561444031	chr1:247362596-247362597	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs76998531	chr1:247362606-247362607	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs111276589	chr1:247362633-247362634	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs371441764	chr1:247362666-247362667	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs574952029	chr1:247362752-247362753	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs533054752	chr1:247362765-247362766	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs551540452	chr1:247362766-247362767	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs542924120	chr1:247362770-247362771	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs566653008	chr1:247362808-247362809	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs540589867	chr1:247362827-247362828	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs376622120	chr1:247362847-247362848	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs116080191	chr1:247362857-247362858	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs572792344	chr1:247362904-247362905	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs201213130	chr1:247362935-247362936	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs146715702	chr1:247362972-247362973	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs567460539	chr1:247362974-247362975	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs76655660	chr1:247362979-247362980	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs55768801	chr1:247362990-247362991	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs556138073	chr1:247362998-247362999	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs545743850	chr1:247363017-247363018	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs12130823	chr1:247363038-247363039	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs184092093	chr1:247363041-247363042	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs72770366	chr1:247363061-247363062	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs572573203	chr1:247363075-247363076	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs542867510	chr1:247363102-247363103	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs561586028	chr1:247363106-247363107	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs61840048	chr1:247363131-247363132	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs72770367	chr1:247363136-247363137	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs12141741	chr1:247363152-247363153	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs12141744	chr1:247363160-247363161	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs112046995	chr1:247363162-247363163	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs560008948	chr1:247363166-247363167	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs145052613	chr1:247363176-247363177	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs7551871	chr1:247363190-247363191	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs567503051	chr1:247363212-247363213	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs547028322	chr1:247363215-247363216	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs376576237	chr1:247363279-247363280	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs537740866	chr1:247363281-247363282	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs1578863	chr1:247363296-247363297	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs571286139	chr1:247363333-247363334	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs538670551	chr1:247363359-247363360	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs564261392	chr1:247363363-247363364	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs553814593	chr1:247363395-247363396	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs11805511	chr1:247363397-247363398	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs536805738	chr1:247363406-247363407	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs554859794	chr1:247363412-247363413	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs374379825	chr1:247363464-247363465	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs544110759	chr1:247363517-247363518	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs11805544	chr1:247363589-247363590	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:30)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Cancer	17060936	CNVD
Multiple myeloma	16616336	CNVD
Cutaneous malignant melanoma	18794153	CNVD
Astrocytoma	17934521	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Breast cancer	20409316	CNVD
Fibroblasts	17951408	CNVD
Lung cancer	17951408	CNVD

Chromatin state (count:214 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247346000-247370200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:247346000-247371800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr1:247351800-247372400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr1:247352000-247368200	ZNF genes & repeats	Liver	Liver
5	chr1:247353000-247367200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:247353000-247368000	ZNF genes & repeats	Primary B cells from cord blood	blood
7	chr1:247353000-247370400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:247353400-247372000	ZNF genes & repeats	GM12878-XiMat	blood
9	chr1:247354000-247371000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:247354800-247371200	Weak transcription	Stomach Mucosa	stomach
11	chr1:247354800-247372400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:247354800-247372400	Weak transcription	Right Ventricle	heart
13	chr1:247356000-247363400	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr1:247356000-247367200	Weak transcription	Brain Substantia Nigra	brain
15	chr1:247356000-247367800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:247356000-247372400	Weak transcription	Brain Anterior Caudate	brain
17	chr1:247356000-247372400	Weak transcription	Fetal Brain Male	brain
18	chr1:247356000-247372600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:247356000-247372600	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:247356200-247372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:247356200-247372400	Weak transcription	Colonic Mucosa	Colon
22	chr1:247356400-247364600	Weak transcription	Aorta	Aorta
23	chr1:247356400-247372400	Weak transcription	Gastric	stomach
24	chr1:247356600-247364400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:247356600-247367800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:247357000-247367400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:247357200-247364000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:247357200-247367000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:247357200-247370800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr1:247357600-247363800	Strong transcription	HUVEC	blood vessel
31	chr1:247357600-247366200	Strong transcription	Adipose Nuclei	Adipose
32	chr1:247357600-247367800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:247357800-247363800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:247357800-247365400	Weak transcription	Brain Germinal Matrix	brain
35	chr1:247357800-247366400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:247358000-247363600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:247358000-247368000	Strong transcription	Fetal Thymus	thymus
38	chr1:247358200-247363400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:247358200-247363600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:247358200-247363800	Strong transcription	Thymus	Thymus
41	chr1:247358200-247364200	Strong transcription	Left Ventricle	heart
42	chr1:247358400-247372400	Weak transcription	Fetal Heart	heart
43	chr1:247358600-247362800	ZNF genes & repeats	Primary T cells from cord blood	blood
44	chr1:247358600-247363600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:247358600-247363800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:247358800-247363600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:247358800-247363600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:247358800-247363600	Strong transcription	Placenta	Placenta
49	chr1:247359000-247363800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:247359000-247364000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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