Variant report

Variant	rs61234123
Chromosome Location	chr15:44827523-44827524
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:10)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:44827216-44827672	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:44827418-44827527	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44580146..44582349-chr15:44827451..44829460,2	MCF-7	breast:

(count:10 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPG11-1	chr15:44827461-44827672	ENSG00000179523.4
2	lnc-SPG11-1	chr15:44827267-44827672	ENSG00000179523.4
3	lnc-SPG11-1	chr15:44825691-44827672	ENSG00000179523.4
4	lnc-SPG11-1	chr15:44827450-44827672	ENSG00000179523.4
5	lnc-SPG11-1	chr15:44827287-44827672	ENSG00000179523.4
6	lnc-SPG11-1	chr15:44826613-44827672	NONHSAT042162
7	lnc-SPG11-1	chr15:44827302-44827672	NONHSAT042166
8	lnc-SPG11-1	chr15:44826703-44827672	NR_034170
9	lnc-SPG11-1	chr15:44826703-44827672	NR_034171
10	lnc-SPG11-1	chr15:44826735-44827672	NONHSAT042163

No data

Variant related genes	Relation type
EIF3J	TF binding region
ENSG00000166734	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10152710	0.94[EUR][1000 genomes]
rs1021800	0.94[EUR][1000 genomes]
rs10467977	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324194	0.82[ASN][1000 genomes]
rs12591178	1.00[EUR][1000 genomes]
rs12591581	0.94[EUR][1000 genomes]
rs12591811	0.94[EUR][1000 genomes]
rs12592995	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593125	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593325	0.94[EUR][1000 genomes]
rs12593686	0.94[EUR][1000 genomes]
rs12593943	0.94[EUR][1000 genomes]
rs12594110	0.94[EUR][1000 genomes]
rs12594139	0.94[EUR][1000 genomes]
rs12594167	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12594621	0.94[EUR][1000 genomes]
rs12594645	0.94[EUR][1000 genomes]
rs12594746	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594905	0.82[ASN][1000 genomes]
rs12594910	0.82[ASN][1000 genomes]
rs12595484	0.94[EUR][1000 genomes]
rs17551416	0.94[EUR][1000 genomes]
rs2055061	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2288341	0.94[EUR][1000 genomes]
rs2288342	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303577	0.94[EUR][1000 genomes]
rs2303578	0.87[EUR][1000 genomes]
rs2412883	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412909	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2433350	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2555353	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2556562	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2556566	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2556567	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28508235	0.94[EUR][1000 genomes]
rs28561508	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899113	0.94[EUR][1000 genomes]
rs2899119	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35555389	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784565	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784567	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809471	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3816928	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3986142	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3986143	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4415978	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4477677	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4577056	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57270586	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58956090	1.00[EUR][1000 genomes]
rs59230801	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59997416	0.94[EUR][1000 genomes]
rs60003667	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60399672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61185650	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61258861	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61278540	0.94[EUR][1000 genomes]
rs61329003	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61501839	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493103	0.82[EUR][1000 genomes]
rs7162671	0.94[EUR][1000 genomes]
rs7162802	0.94[EUR][1000 genomes]
rs7163287	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7163529	0.94[EUR][1000 genomes]
rs7164709	0.94[EUR][1000 genomes]
rs7166278	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167752	0.94[EUR][1000 genomes]
rs7167870	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7169333	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7170248	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172106	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175200	0.94[EUR][1000 genomes]
rs7178318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179390	0.82[ASN][1000 genomes]
rs7179894	0.94[EUR][1000 genomes]
rs7181772	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7183109	0.89[EUR][1000 genomes]
rs73417597	0.82[ASN][1000 genomes]
rs8023453	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024623	0.94[EUR][1000 genomes]
rs8024805	0.94[EUR][1000 genomes]
rs8025727	0.94[EUR][1000 genomes]
rs8025876	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025955	0.94[EUR][1000 genomes]
rs8026945	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027036	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028509	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8028907	0.82[EUR][1000 genomes]
rs8032079	0.94[EUR][1000 genomes]
rs8037395	0.82[EUR][1000 genomes]
rs883943	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9672237	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9673085	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9806725	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
3	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44721000-44828000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:44750200-44828000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:44778000-44827800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:44778000-44827800	Weak transcription	Psoas Muscle	Psoas
5	chr15:44779800-44827800	Weak transcription	Aorta	Aorta
6	chr15:44783200-44827800	Weak transcription	NHLF	lung
7	chr15:44783600-44828000	Weak transcription	HSMMtube	muscle
8	chr15:44790800-44827800	Weak transcription	Small Intestine	intestine
9	chr15:44796200-44827800	Weak transcription	Brain Anterior Caudate	brain
10	chr15:44796200-44828000	Weak transcription	Brain Substantia Nigra	brain
11	chr15:44796400-44827800	Weak transcription	Esophagus	oesophagus
12	chr15:44796400-44827800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:44797000-44828000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:44798800-44828000	Weak transcription	A549	lung
15	chr15:44800800-44828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:44807400-44828200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:44812800-44827800	Weak transcription	Spleen	Spleen
18	chr15:44814000-44827600	Weak transcription	NH-A	brain
19	chr15:44815800-44827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:44815800-44828000	Weak transcription	Fetal Kidney	kidney
21	chr15:44816000-44827800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:44816400-44827800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:44816600-44828000	Weak transcription	Brain Angular Gyrus	brain
24	chr15:44816600-44828000	Weak transcription	Thymus	Thymus
25	chr15:44816800-44827600	Weak transcription	HUVEC	blood vessel
26	chr15:44817400-44827600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:44817400-44827600	Weak transcription	GM12878-XiMat	blood
28	chr15:44817600-44827600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:44817600-44827600	Weak transcription	Primary B cells from cord blood	blood
30	chr15:44817600-44827600	Weak transcription	Primary T cells from cord blood	blood
31	chr15:44817600-44827600	Weak transcription	Fetal Brain Male	brain
32	chr15:44817600-44828000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:44817600-44828200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:44817800-44827600	Weak transcription	Fetal Intestine Large	intestine
35	chr15:44817800-44827800	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:44818000-44827600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:44819400-44827800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:44819400-44827800	Weak transcription	Dnd41	blood
39	chr15:44819800-44827600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:44819800-44827600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:44819800-44828000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:44820000-44827600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:44820000-44827800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:44820000-44827800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:44820200-44827800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:44820400-44827600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:44820400-44827800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr15:44820400-44827800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr15:44821600-44827800	Weak transcription	Right Atrium	heart
50	chr15:44822400-44827600	Strong transcription	Fetal Stomach	stomach

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