Variant report

Variant	rs4478072
Chromosome Location	chr3:53106125-53106126
allele	G/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:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52846403..52849338-chr3:53105437..53107492,2	MCF-7	breast:
2	chr3:52939978..52942198-chr3:53105918..53108095,2	K562	blood:
3	chr3:53079186..53081948-chr3:53104941..53107753,3	MCF-7	breast:
4	chr3:53078527..53081338-chr3:53105263..53108588,3	MCF-7	breast:
5	chr3:53105521..53108004-chr3:53109136..53111308,2	K562	blood:
6	chr3:53106005..53108622-chr3:53188208..53190732,2	MCF-7	breast:
7	chr3:53099455..53102184-chr3:53105815..53107465,2	K562	blood:
8	chr3:53053108..53056030-chr3:53104834..53107226,3	K562	blood:
9	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
ENSG00000163932	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10510761	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11706035	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11707575	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707780	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11710292	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710394	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11710707	0.84[EUR][1000 genomes]
rs11711773	0.88[EUR][1000 genomes]
rs11712653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11713171	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11713206	0.84[EUR][1000 genomes]
rs11713290	0.84[EUR][1000 genomes]
rs11713859	0.87[EUR][1000 genomes]
rs11713926	0.88[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11714037	0.84[EUR][1000 genomes]
rs11714876	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs11714902	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11717132	0.84[EUR][1000 genomes]
rs11717619	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11717715	0.84[EUR][1000 genomes]
rs11718388	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11718538	0.82[EUR][1000 genomes]
rs11718752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718834	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11720191	0.84[EUR][1000 genomes]
rs13058817	0.87[EUR][1000 genomes]
rs13069006	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13072395	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13072457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13074524	0.84[EUR][1000 genomes]
rs13078834	0.84[EUR][1000 genomes]
rs13078971	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084937	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13085514	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13085544	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13088281	0.88[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs13091844	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13092352	0.82[EUR][1000 genomes]
rs13320044	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1346719	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs1560333	1.00[JPT][hapmap]
rs17052727	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2336540	0.84[EUR][1000 genomes]
rs2336541	0.84[EUR][1000 genomes]
rs2564926	0.98[EUR][1000 genomes]
rs2581807	0.98[EUR][1000 genomes]
rs3097417	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34121720	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34238610	0.89[EUR][1000 genomes]
rs34244302	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34313969	0.84[EUR][1000 genomes]
rs34340609	0.94[EUR][1000 genomes]
rs34493168	0.84[EUR][1000 genomes]
rs34754279	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34872575	0.84[EUR][1000 genomes]
rs34933390	0.84[EUR][1000 genomes]
rs34943350	0.84[EUR][1000 genomes]
rs34979715	0.89[EUR][1000 genomes]
rs35076015	0.89[EUR][1000 genomes]
rs35163227	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35174175	0.89[EUR][1000 genomes]
rs35378159	0.84[EUR][1000 genomes]
rs35384050	0.84[EUR][1000 genomes]
rs35385050	0.84[EUR][1000 genomes]
rs35507120	0.89[EUR][1000 genomes]
rs35720014	0.84[EUR][1000 genomes]
rs35737577	0.84[EUR][1000 genomes]
rs35849389	0.84[EUR][1000 genomes]
rs36090694	0.84[EUR][1000 genomes]
rs3796352	1.00[CEU][hapmap]
rs3806692	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs3821872	0.91[EUR][1000 genomes]
rs58515094	0.84[EUR][1000 genomes]
rs58660500	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59583591	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60887045	0.84[EUR][1000 genomes]
rs60942590	0.84[EUR][1000 genomes]
rs61172708	0.84[EUR][1000 genomes]
rs6445555	0.86[EUR][1000 genomes]
rs6445556	0.93[EUR][1000 genomes]
rs6445557	0.93[EUR][1000 genomes]
rs71301804	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71301808	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71301809	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71301811	0.98[EUR][1000 genomes]
rs71301814	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71301815	0.82[ASN][1000 genomes]
rs71301816	0.90[ASN][1000 genomes]
rs71617204	0.89[EUR][1000 genomes]
rs750474	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7622420	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625448	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640293	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9756317	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs9875573	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4478072	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53102200-53106400	Weak transcription	Colonic Mucosa	Colon
2	chr3:53102400-53106200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:53104000-53106400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:53104200-53106400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:53104200-53106400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:53104200-53106400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:53104400-53106400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:53105200-53106400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:53105200-53106600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:53105400-53106400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:53105400-53106400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr3:53105400-53106400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:53105400-53106400	Enhancers	Right Ventricle	heart
14	chr3:53105600-53106200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:53105600-53106200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:53105600-53106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:53105600-53106400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:53105600-53106400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr3:53105600-53106400	Enhancers	Fetal Muscle Leg	muscle
20	chr3:53105600-53106400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:53105600-53106600	Flanking Active TSS	HepG2	liver
22	chr3:53105600-53106800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:53105800-53106400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:53105800-53106400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:53105800-53106400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:53105800-53106400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:53105800-53106400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr3:53105800-53106400	Enhancers	Brain Angular Gyrus	brain
29	chr3:53105800-53106400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:53105800-53106400	Enhancers	Fetal Heart	heart
31	chr3:53105800-53106400	Enhancers	Fetal Intestine Small	intestine
32	chr3:53105800-53106400	Enhancers	Fetal Thymus	thymus
33	chr3:53105800-53106400	Enhancers	K562	blood
34	chr3:53105800-53106600	Enhancers	Primary B cells from peripheral blood	blood
35	chr3:53105800-53106600	Enhancers	Left Ventricle	heart
36	chr3:53106000-53106200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:53106000-53106200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:53106000-53106200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:53106000-53106200	Enhancers	Brain Hippocampus Middle	brain
40	chr3:53106000-53106200	Enhancers	Colon Smooth Muscle	Colon
41	chr3:53106000-53106200	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr3:53106000-53106200	Bivalent Enhancer	Placenta	Placenta
43	chr3:53106000-53106200	Enhancers	Stomach Smooth Muscle	stomach
44	chr3:53106000-53106200	Enhancers	Spleen	Spleen
45	chr3:53106000-53106200	Enhancers	Dnd41	blood
46	chr3:53106000-53106400	Enhancers	Primary T cells from cord blood	blood
47	chr3:53106000-53106400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:53106000-53106400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:53106000-53106400	Enhancers	Adipose Nuclei	Adipose
50	chr3:53106000-53106400	Enhancers	Brain Germinal Matrix	brain

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