Variant report

Variant	nsv877902
Chromosome Location	chr3:164370044-164435296
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	BRCA1	chr3:164401316-164401654	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr3:164399826-164399926	HepG2	liver:	n/a	chr3:164399882-164399893
3	CEBPB	chr3:164370379-164370516	K562	blood:	n/a	chr3:164370444-164370457
4	CEBPB	chr3:164412753-164413107	HepG2	liver:	n/a	chr3:164412919-164412930
5	CEBPB	chr3:164401241-164401844	MCF-7	breast:	n/a	chr3:164401507-164401524 chr3:164401512-164401523
6	CEBPB	chr3:164401328-164401794	MCF-7	breast:	n/a	chr3:164401507-164401524 chr3:164401512-164401523
7	CEBPB	chr3:164412763-164413091	Hela-S3	cervix:	n/a	chr3:164412919-164412930
8	CEBPB	chr3:164412719-164413128	MCF-7	breast:	n/a	chr3:164412919-164412930
9	CEBPB	chr3:164397276-164397628	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr3:164401266-164401790	Hela-S3	cervix:	n/a	chr3:164401507-164401524 chr3:164401512-164401523
11	CEBPB	chr3:164412780-164413072	A549	lung:	n/a	chr3:164412919-164412930
12	CHD2	chr3:164409943-164409953	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:164391640-164391790	RPTEC	kidney:	n/a	chr3:164391727-164391736
14	CTCF	chr3:164391660-164391810	HEEpiC	esophagus:	n/a	chr3:164391727-164391736
15	CTCF	chr3:164391660-164391810	MCF-7	breast:	n/a	chr3:164391727-164391736
16	CTCF	chr3:164391720-164391870	RPTEC	kidney:	n/a	chr3:164391727-164391736
17	CTCF	chr3:164391487-164391917	MCF-7	breast:	n/a	chr3:164391727-164391736
18	CTCF	chr3:164391640-164391790	HepG2	liver:	n/a	chr3:164391727-164391736
19	CTCF	chr3:164391620-164391770	HFF	foreskin:	n/a	chr3:164391727-164391736
20	CTCF	chr3:164391600-164391750	Caco-2	colon:	n/a	chr3:164391727-164391736
21	CTCF	chr3:164391620-164391770	SK-N-SH_RA	brain:	n/a	chr3:164391727-164391736
22	CTCF	chr3:164391664-164391791	MCF-7	breast:	n/a	chr3:164391727-164391736
23	CTCF	chr3:164391620-164391770	HCT-116	colon:	n/a	chr3:164391727-164391736
24	CTCF	chr3:164391660-164391803	HepG2	liver:	n/a	chr3:164391727-164391736
25	CTCF	chr3:164391670-164391769	HepG2	liver:	n/a	chr3:164391727-164391736
26	CTCF	chr3:164411695-164411744	Lung_OC	lung:	n/a	n/a
27	CTCF	chr3:164391600-164391750	HBMEC	blood vessel:	n/a	chr3:164391727-164391736
28	CTCF	chr3:164391658-164391757	GM13977	blood:	n/a	chr3:164391727-164391736
29	CTCF	chr3:164391640-164391790	HEK293	kidney:	n/a	chr3:164391727-164391736
30	CTCF	chr3:164391622-164391809	Medullo	brain:	n/a	chr3:164391727-164391736
31	CTCF	chr3:164391672-164391780	SK-N-SH_RA	brain:	n/a	chr3:164391727-164391736
32	CTCF	chr3:164391660-164391810	HRE	kidney:	n/a	chr3:164391727-164391736
33	CTCF	chr3:164391620-164391770	Hela-S3	cervix:	n/a	chr3:164391727-164391736
34	CTCF	chr3:164391560-164391886	MCF-7	breast:	n/a	chr3:164391727-164391736
35	CTCF	chr3:164409900-164410050	GM12869	blood:	n/a	n/a
36	CTCF	chr3:164402258-164402305	MCF-7	breast:	n/a	n/a
37	CTCF	chr3:164391700-164391850	Hela-S3	cervix:	n/a	chr3:164391727-164391736
38	CTCF	chr3:164391580-164391730	GM12872	blood:	n/a	n/a
39	CTCF	chr3:164391640-164391790	Caco-2	colon:	n/a	chr3:164391727-164391736
40	CTCF	chr3:164391568-164391875	GM12878	blood:	n/a	chr3:164391727-164391736
41	CTCF	chr3:164391740-164391890	HRE	kidney:	n/a	n/a
42	CTCF	chr3:164391680-164391830	HMEC	breast:	n/a	chr3:164391727-164391736
43	CTCF	chr3:164391620-164391770	HMF	breast:	n/a	chr3:164391727-164391736
44	CTCF	chr3:164391641-164391798	Hela-S3	cervix:	n/a	chr3:164391727-164391736
45	CTCF	chr3:164391600-164391750	HMF	breast:	n/a	chr3:164391727-164391736
46	CTCF	chr3:164391660-164391810	BE2_C	brain:	n/a	chr3:164391727-164391736
47	CTCF	chr3:164391680-164391830	MCF-7	breast:	n/a	chr3:164391727-164391736
48	CTCF	chr3:164370022-164370107	GM13976	blood:	n/a	n/a
49	CTCF	chr3:164391680-164391830	HRPEpiC	eye:	n/a	chr3:164391727-164391736
50	CTCF	chr3:164391620-164391770	HepG2	liver:	n/a	chr3:164391727-164391736

No.	Distal block	Cell Line	Cell type
1	chr3:164382723..164384365-chr3:164390839..164393550,2	MCF-7	breast:
2	chr3:164382723..164384365-chr3:164390839..164393550,2	MCF-7	breast:
3	chr3:164355558..164357908-chr3:164371177..164373033,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SI-2	chr3:164401605-164401689	XLOC_003313
2	lnc-SI-1	chr3:164431883-164432270	XLOC_003314
3	lnc-SI-5	chr3:164387550-164388087	l_2521_chr3:164387549-164449856_testes
4	lnc-SERPINI1-9	chr3:164405416-164405657	XLOC_002900
5	lnc-SI-5	chr3:164420366-164420516	l_2521_chr3:164387549-164449856_testes
6	lnc-SI-5	chr3:164420522-164420669	l_2521_chr3:164387549-164449856_testes
7	lnc-SERPINI1-9	chr3:164405416-164405657	XLOC_002900
8	lnc-SI-2	chr3:164388666-164389019	XLOC_003313
9	lnc-SERPINI1-9	chr3:164405416-164405798	XLOC_002900
10	lnc-SI-5	chr3:164402020-164402099	l_2521_chr3:164387549-164449856_testes
11	lnc-SI-1	chr3:164431889-164432270	XLOC_003314
12	lnc-SI-2	chr3:164403812-164403864	XLOC_003313
13	lnc-SI-5	chr3:164400353-164400433	l_2521_chr3:164387549-164449856_testes
14	lnc-SI-2	chr3:164402987-164403070	XLOC_003313
15	lnc-SI-5	chr3:164400110-164400236	l_2521_chr3:164387549-164449856_testes

Variant related genes	Relation type
ENSG00000241636	TF binding region
COL3A1	miRNA target sites
C1D	miRNA target sites
AKT1	miRNA target sites
RORC	miRNA target sites
AKAP13	miRNA target sites

Extended variants
information (count: 359 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:359 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs73028452	chr3:164375204-164375205	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs559164968	chr3:164375262-164375263	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs530164198	chr3:164375267-164375268	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs532850894	chr3:164375310-164375311	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs143583078	chr3:164375313-164375314	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs191973031	chr3:164375383-164375384	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs538836242	chr3:164375401-164375402	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs551090635	chr3:164375431-164375432	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs146828629	chr3:164375467-164375468	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs148529311	chr3:164375477-164375478	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs541296551	chr3:164375513-164375514	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs59302432	chr3:164375514-164375515	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs574358656	chr3:164375563-164375564	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs527408599	chr3:164375646-164375647	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs373317996	chr3:164375677-164375678	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs563394245	chr3:164375695-164375696	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs377684256	chr3:164375697-164375698	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs184953767	chr3:164375749-164375750	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs546031879	chr3:164375794-164375795	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs117432252	chr3:164375826-164375827	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs528419772	chr3:164375834-164375835	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs548434560	chr3:164375845-164375846	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs560658634	chr3:164375850-164375851	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs532857702	chr3:164375861-164375862	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs16848471	chr3:164375880-164375881	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs550044509	chr3:164375895-164375896	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs569116427	chr3:164375944-164375945	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs189425387	chr3:164375945-164375946	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs142938003	chr3:164375961-164375962	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs151082193	chr3:164376039-164376040	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs141105990	chr3:164376058-164376059	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs535019774	chr3:164376066-164376067	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs530534663	chr3:164376068-164376069	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs115313598	chr3:164376075-164376076	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs574396731	chr3:164376134-164376135	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs78619660	chr3:164376139-164376140	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs149840523	chr3:164376147-164376148	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs577017480	chr3:164376180-164376181	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs545888954	chr3:164376236-164376237	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs55657015	chr3:164376254-164376255	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs191600215	chr3:164376270-164376271	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs541789227	chr3:164376288-164376289	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs59570876	chr3:164376301-164376302	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs183704503	chr3:164376320-164376321	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs550150154	chr3:164376369-164376370	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs569685428	chr3:164376380-164376381	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs547171941	chr3:164376401-164376402	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs552237155	chr3:164376403-164376404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs567096320	chr3:164376421-164376422	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs535218269	chr3:164376515-164376516	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Sudden cardiac death	19188705	CNVD
Mantle cell lymphoma	19029149	CNVD
Malformation	19546859	CNVD
Schizophrenia	19546859	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	20164919	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
small cell lung cancer	20016488	CNVD
Schizophrenia	23813976	CNVD
Breast cancer	21364760	CNVD
Chordoma	21215367	CNVD

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:164375200-164376400	Enhancers	Fetal Brain Male	brain
2	chr3:164375600-164376400	Enhancers	Fetal Brain Female	brain
3	chr3:164375800-164376600	Enhancers	Colon Smooth Muscle	Colon
4	chr3:164376000-164376400	Enhancers	Pancreas	Pancrea
5	chr3:164376200-164376400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:164394600-164395000	Enhancers	Hela-S3	cervix
7	chr3:164395200-164395600	Enhancers	Hela-S3	cervix
8	chr3:164401200-164401600	Enhancers	Hela-S3	cervix
9	chr3:164404000-164404400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:164404400-164404800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:164404800-164405200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:164404800-164405200	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:164405000-164405600	Active TSS	Brain Anterior Caudate	brain
14	chr3:164405000-164405600	Enhancers	Brain Hippocampus Middle	brain
15	chr3:164405200-164405400	Enhancers	Brain Angular Gyrus	brain
16	chr3:164405200-164405400	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:164405200-164405600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:164405400-164405600	Active TSS	Brain Cingulate Gyrus	brain
19	chr3:164405600-164405800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:164407600-164407800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:164412800-164413200	Enhancers	Brain Substantia Nigra	brain
22	chr3:164413200-164413600	Active TSS	Brain Substantia Nigra	brain
23	chr3:164420400-164420800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:164429000-164429600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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