Variant report

Variant	esv3693107
Chromosome Location	chr12:9010671-9013783
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:8834370..8834975-chr12:9013092..9013685,2	MCF-7	breast:
2	chr12:9008234..9009916-chr12:9010931..9013875,2	MCF-7	breast:
3	chr12:9011608..9013932-chr12:9031539..9033182,2	MCF-7	breast:
4	chr12:8932743..8934022-chr12:9012782..9013946,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-M6PR-5	chr12:9010526-9010872	NONHSAT026375

Variant related genes	Relation type
ENSG00000166535	chromatin interactions

Extended variants
information (count: 74 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:74 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11612600	chr12:9010671-9010672	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs371934378	chr12:9010681-9010682	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs61745125	chr12:9010686-9010687	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs200006435	chr12:9010703-9010704	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs371398250	chr12:9010731-9010732	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs375930372	chr12:9010738-9010739	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs192923792	chr12:9010739-9010740	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs184698806	chr12:9010745-9010746	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs12304546	chr12:9010806-9010807	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs148454477	chr12:9010870-9010871	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs141912625	chr12:9010888-9010889	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs34102735	chr12:9010936-9010937	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs189671128	chr12:9010949-9010950	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs11610808	chr12:9010969-9010970	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs56273384	chr12:9011059-9011060	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs116138326	chr12:9011088-9011089	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs191302345	chr12:9011164-9011165	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs79794342	chr12:9011256-9011257	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs77487303	chr12:9011398-9011399	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs183928287	chr12:9011442-9011443	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs143555077	chr12:9011459-9011460	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs111624644	chr12:9011462-9011463	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs7488933	chr12:9011512-9011513	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs189389071	chr12:9011609-9011610	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs531391533	chr12:9011626-9011627	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs12302462	chr12:9011644-9011645	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs146882342	chr12:9011666-9011667	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs367604594	chr12:9011768-9011769	Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs73038791	chr12:9011898-9011899	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs60731237	chr12:9011899-9011900	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs73038794	chr12:9011901-9011902	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs539632520	chr12:9011940-9011941	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs534236178	chr12:9011964-9011965	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs139776155	chr12:9012084-9012085	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs554164862	chr12:9012151-9012152	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs150061678	chr12:9012338-9012339	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs145376530	chr12:9012409-9012410	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs540108025	chr12:9012446-9012447	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs2377609	chr12:9012521-9012522	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs149181258	chr12:9012559-9012560	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs374911575	chr12:9012600-9012601	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs79708571	chr12:9012643-9012644	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs182087362	chr12:9012754-9012755	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs368141157	chr12:9012779-9012780	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs759105	chr12:9012794-9012795	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs6487418	chr12:9012878-9012879	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs55823587	chr12:9012933-9012934	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs554695750	chr12:9012981-9012982	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs34241610	chr12:9013055-9013056	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs574409058	chr12:9013058-9013059	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:77)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Hepatocellular carcinoma	16750200	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Epilepsy	21858020	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Myelofibrosis	22110671	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
craniofacial dysmorphism	21918468	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Alzheimer''s disease	17160897	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	21251322	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8982200-9022000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:8983400-9017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:8987600-9040000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:8987800-9012800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:8988200-9012800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:8994800-9016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:8996000-9040000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:8998800-9014600	Weak transcription	Right Atrium	heart
9	chr12:8999000-9016400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:9000800-9012400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:9001200-9011600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:9005000-9013400	Weak transcription	Brain Anterior Caudate	brain
13	chr12:9005200-9017800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:9007000-9029600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:9007200-9027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:9008000-9011400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:9009000-9011200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:9009200-9012800	Weak transcription	K562	blood
19	chr12:9009600-9012600	Strong transcription	Esophagus	oesophagus
20	chr12:9010200-9011400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:9011400-9011800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:9011400-9012800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:9011600-9011800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:9011800-9021600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:9011800-9029800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:9012600-9020400	Weak transcription	Esophagus	oesophagus
27	chr12:9012800-9013600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr12:9012800-9013600	Enhancers	K562	blood
29	chr12:9012800-9013800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:9013000-9013400	Enhancers	Placenta	Placenta
31	chr12:9013000-9013800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:9013400-9013600	Enhancers	Brain Anterior Caudate	brain
33	chr12:9013400-9013600	Enhancers	Spleen	Spleen
34	chr12:9013600-9019200	Weak transcription	K562	blood
35	chr12:9013600-9029400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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