Variant report

Variant	rs71327003
Chromosome Location	chr3:46036521-46036522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:45979978..45982491-chr3:46035904..46038054,2	MCF-7	breast:
2	chr3:45639893..45641594-chr3:46034221..46037019,2	K562	blood:
3	chr3:46035149..46036764-chr3:46100668..46103208,2	K562	blood:
4	chr3:45999931..46002048-chr3:46035446..46037262,2	MCF-7	breast:
5	chr3:46019979..46023374-chr3:46034093..46037294,5	K562	blood:
6	chr3:46036059..46037983-chr3:46447594..46449867,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XCR1-2	chr3:46033520-46037161	ucscGeneNc_uc003cpd_1

No data

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction
ENSG00000223552	Chromatin interaction
ENSG00000172215	Chromatin interaction
ENSG00000121797	Chromatin interaction

Extended variants
information (count: 172 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs12108042	0.88[EUR][1000 genomes]
rs13059238	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13060287	0.96[EUR][1000 genomes]
rs13063527	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13063635	0.90[AMR][1000 genomes]
rs13066062	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13066516	0.87[EUR][1000 genomes]
rs13068410	0.88[EUR][1000 genomes]
rs13068570	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13069079	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13069742	0.89[EUR][1000 genomes]
rs13071283	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13072267	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13074382	0.96[EUR][1000 genomes]
rs13075528	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13075758	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13078739	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13079869	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13081151	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13081213	0.96[EUR][1000 genomes]
rs13082697	0.96[EUR][1000 genomes]
rs13085367	0.90[AMR][1000 genomes]
rs13089554	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13089855	0.98[EUR][1000 genomes]
rs13090194	0.96[EUR][1000 genomes]
rs13091868	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13093179	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13094262	0.88[EUR][1000 genomes]
rs13095602	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13095717	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13096741	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13097556	0.96[EUR][1000 genomes]
rs13099120	0.87[EUR][1000 genomes]
rs13433997	0.96[EUR][1000 genomes]
rs1491950	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1491951	0.89[EUR][1000 genomes]
rs17214952	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17215008	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17215981	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17280623	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17282175	0.86[AMR][1000 genomes]
rs17282238	0.84[AMR][1000 genomes]
rs17330872	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17714101	0.84[EUR][1000 genomes]
rs17714228	0.84[EUR][1000 genomes]
rs17764980	0.84[EUR][1000 genomes]
rs1994491	0.85[EUR][1000 genomes]
rs1994492	0.86[EUR][1000 genomes]
rs1994493	0.86[EUR][1000 genomes]
rs2088690	0.96[EUR][1000 genomes]
rs2088692	0.96[EUR][1000 genomes]
rs2088693	0.88[EUR][1000 genomes]
rs2102055	0.96[EUR][1000 genomes]
rs2102056	0.91[EUR][1000 genomes]
rs2171531	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2230322	0.96[EUR][1000 genomes]
rs2373087	0.87[EUR][1000 genomes]
rs33910087	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34000569	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34047915	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34068335	0.86[EUR][1000 genomes]
rs34093271	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34127208	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34168660	0.96[EUR][1000 genomes]
rs34283240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34324101	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34339943	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34340587	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34381952	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34438204	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34442130	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34452002	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34460587	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34492478	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34493660	0.98[EUR][1000 genomes]
rs34562820	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34584867	0.96[EUR][1000 genomes]
rs34619093	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34679077	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34718164	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34754340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34766614	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34774687	0.96[EUR][1000 genomes]
rs34805664	0.85[EUR][1000 genomes]
rs34836513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34849862	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34863575	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34867672	0.88[EUR][1000 genomes]
rs34924300	0.86[EUR][1000 genomes]
rs35028116	0.88[EUR][1000 genomes]
rs35110864	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35159820	0.96[EUR][1000 genomes]
rs35161099	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35209528	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35334665	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35454877	0.96[EUR][1000 genomes]
rs35464221	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35477280	0.87[EUR][1000 genomes]
rs35501575	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35516580	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35525815	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35539222	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35581648	0.90[AMR][1000 genomes]
rs35669129	0.96[EUR][1000 genomes]
rs35751180	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35772789	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35814488	0.96[EUR][1000 genomes]
rs35827997	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35831747	0.87[EUR][1000 genomes]
rs35855315	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35883205	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35921206	0.96[EUR][1000 genomes]
rs35930050	0.96[EUR][1000 genomes]
rs36023124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36039366	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36040135	0.96[EUR][1000 genomes]
rs36057789	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36122610	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3851346	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41289616	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41289622	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4362758	0.96[EUR][1000 genomes]
rs4373103	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4388012	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4683166	0.88[EUR][1000 genomes]
rs55875328	0.98[EUR][1000 genomes]
rs55920693	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56332428	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60019065	0.96[EUR][1000 genomes]
rs61556067	0.98[EUR][1000 genomes]
rs61650989	0.98[EUR][1000 genomes]
rs67200151	0.98[EUR][1000 genomes]
rs6780028	0.96[EUR][1000 genomes]
rs6785091	0.89[EUR][1000 genomes]
rs6790866	0.96[EUR][1000 genomes]
rs6791016	0.96[EUR][1000 genomes]
rs67937868	0.98[EUR][1000 genomes]
rs68087193	0.93[EUR][1000 genomes]
rs71325091	0.80[EUR][1000 genomes]
rs71325092	0.84[EUR][1000 genomes]
rs71325095	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71325096	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71325098	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71325100	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71325101	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71325102	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327006	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71327007	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71327009	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71327010	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71327014	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327015	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327017	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327021	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327023	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327024	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327025	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327027	0.90[AMR][1000 genomes]
rs71615438	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642229	0.86[EUR][1000 genomes]
rs7642320	0.88[EUR][1000 genomes]
rs7652478	0.88[EUR][1000 genomes]
rs876668	0.96[EUR][1000 genomes]
rs9824651	0.89[EUR][1000 genomes]
rs9825081	0.89[EUR][1000 genomes]
rs9845382	0.89[EUR][1000 genomes]
rs9877748	0.89[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46034600-46037000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
2	chr3:46034800-46036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:46035800-46036600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:46035800-46036800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:46035800-46037000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr3:46035800-46037600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:46035800-46037800	Active TSS	Right Atrium	heart
8	chr3:46036000-46036600	Active TSS	Fetal Brain Female	brain
9	chr3:46036000-46037000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:46036000-46037000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr3:46036000-46037400	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:46036000-46037400	Active TSS	NH-A	brain
13	chr3:46036000-46037600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:46036000-46037600	Active TSS	Aorta	Aorta
15	chr3:46036000-46037600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr3:46036000-46037600	Active TSS	Ovary	ovary
17	chr3:46036000-46037600	Active TSS	Hela-S3	cervix
18	chr3:46036000-46037800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr3:46036000-46037800	Active TSS	Colonic Mucosa	Colon
20	chr3:46036000-46037800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr3:46036000-46037800	Active TSS	Right Ventricle	heart
22	chr3:46036000-46038000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:46036200-46036600	Enhancers	Placenta	Placenta
24	chr3:46036200-46036600	Flanking Active TSS	Small Intestine	intestine
25	chr3:46036200-46036600	Enhancers	Spleen	Spleen
26	chr3:46036200-46036600	Active TSS	HepG2	liver
27	chr3:46036200-46036600	Flanking Active TSS	NHEK	skin
28	chr3:46036200-46036800	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr3:46036200-46036800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr3:46036200-46036800	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr3:46036200-46037000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:46036200-46037000	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr3:46036200-46037000	Flanking Active TSS	Fetal Muscle Trunk	muscle
34	chr3:46036200-46037400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:46036200-46037400	Active TSS	Muscle Satellite Cultured Cells	--
36	chr3:46036200-46037400	Active TSS	Left Ventricle	heart
37	chr3:46036200-46037400	Active TSS	HMEC	breast
38	chr3:46036200-46037600	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr3:46036200-46037600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:46036200-46037600	Active TSS	Fetal Intestine Large	intestine
41	chr3:46036200-46037600	Active TSS	Gastric	stomach
42	chr3:46036200-46037800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:46036200-46037800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr3:46036200-46037800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:46036200-46037800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:46036200-46037800	Active TSS	Psoas Muscle	Psoas
47	chr3:46036200-46038000	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:46036200-46038000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:46036200-46038000	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr3:46036200-46038000	Active TSS	Fetal Kidney	kidney

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