Variant report

Variant	rs1991567
Chromosome Location	chr3:53105779-53105780
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	chr3:52846403..52849338-chr3:53105437..53107492,2	MCF-7	breast:
2	chr3:53079186..53081948-chr3:53104941..53107753,3	MCF-7	breast:
3	chr3:53078527..53081338-chr3:53105263..53108588,3	MCF-7	breast:
4	chr3:53105521..53108004-chr3:53109136..53111308,2	K562	blood:
5	chr3:53053108..53056030-chr3:53104834..53107226,3	K562	blood:
6	chr3:52933827..52935933-chr3:53105479..53107077,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFT1-3	chr3:53100873-53109103	NONHSAT089980

No data

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12486028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12633559	1.00[AMR][1000 genomes]
rs13064076	1.00[AMR][1000 genomes]
rs13066997	1.00[EUR][1000 genomes]
rs1986738	1.00[EUR][1000 genomes]
rs1986739	1.00[EUR][1000 genomes]
rs2001733	1.00[EUR][1000 genomes]
rs2001734	1.00[EUR][1000 genomes]
rs2246888	1.00[EUR][1000 genomes]
rs2246889	1.00[EUR][1000 genomes]
rs2336159	1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336556	1.00[EUR][1000 genomes]
rs2336557	1.00[EUR][1000 genomes]
rs2336559	1.00[EUR][1000 genomes]
rs2564925	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2564927	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2564943	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2564946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2581781	1.00[AMR][1000 genomes]
rs2581814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs4234637	1.00[EUR][1000 genomes]
rs4234640	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687557	1.00[EUR][1000 genomes]
rs4687670	1.00[EUR][1000 genomes]
rs4687671	1.00[EUR][1000 genomes]
rs4687674	1.00[EUR][1000 genomes]
rs4687675	1.00[EUR][1000 genomes]
rs4687685	1.00[EUR][1000 genomes]
rs4687690	1.00[EUR][1000 genomes]
rs55654539	1.00[AMR][1000 genomes]
rs57430179	1.00[EUR][1000 genomes]
rs58561805	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59094265	1.00[EUR][1000 genomes]
rs59234300	1.00[AMR][1000 genomes]
rs61274383	1.00[EUR][1000 genomes]
rs61641433	1.00[EUR][1000 genomes]
rs6445540	1.00[EUR][1000 genomes]
rs6445542	1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6795138	1.00[EUR][1000 genomes]
rs6797070	1.00[EUR][1000 genomes]
rs72961745	1.00[EUR][1000 genomes]
rs72961755	1.00[EUR][1000 genomes]
rs72967404	1.00[EUR][1000 genomes]
rs72967414	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7629350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637212	1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs9682449	1.00[EUR][1000 genomes]
rs9682819	1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9833487	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9869545	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9877711	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53098400-53106000	Weak transcription	Spleen	Spleen
2	chr3:53100400-53105800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:53100600-53106000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:53102200-53105800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:53102200-53105800	Weak transcription	K562	blood
6	chr3:53102200-53106000	Weak transcription	Fetal Intestine Large	intestine
7	chr3:53102200-53106400	Weak transcription	Colonic Mucosa	Colon
8	chr3:53102400-53106000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:53102400-53106200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:53104000-53106400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:53104200-53106000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:53104200-53106400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:53104200-53106400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:53104200-53106400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:53104400-53106400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:53105200-53106400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr3:53105200-53106600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:53105400-53106400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:53105400-53106400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:53105400-53106400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:53105400-53106400	Enhancers	Right Ventricle	heart
22	chr3:53105600-53106200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:53105600-53106200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:53105600-53106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:53105600-53106400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:53105600-53106400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr3:53105600-53106400	Enhancers	Fetal Muscle Leg	muscle
28	chr3:53105600-53106400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:53105600-53106600	Flanking Active TSS	HepG2	liver
30	chr3:53105600-53106800	Enhancers	Placenta Amnion	Placenta Amnion

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