Variant report

Variant	rs7937410
Chromosome Location	chr11:47206082-47206083
allele	C/G
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	POLR2A	chr11:47204907-47209088	HepG2	liver:	n/a	n/a
2	YY1	chr11:47205999-47208165	HepG2	liver:	n/a	chr11:47208079-47208090 chr11:47207478-47207492 chr11:47207856-47207870 chr11:47207861-47207870 chr11:47207011-47207022 chr11:47207117-47207131
3	MAX	chr11:47205478-47209283	HepG2	liver:	n/a	chr11:47207005-47207015 chr11:47208870-47208880 chr11:47207105-47207115 chr11:47207475-47207485 chr11:47207774-47207784 chr11:47208558-47208565
4	HDAC2	chr11:47206076-47206766	HepG2	liver:	n/a	chr11:47206500-47206509
5	HNF4A	chr11:47205752-47207458	HepG2	liver:	n/a	chr11:47206582-47206595 chr11:47205795-47205809 chr11:47206583-47206595 chr11:47206580-47206598 chr11:47205797-47205805 chr11:47205796-47205809
6	RFX5	chr11:47206051-47207396	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:47205622-47209522	HepG2	liver:	n/a	n/a
8	HEY1	chr11:47205552-47206094	HepG2	liver:	n/a	n/a
9	RCOR1	chr11:47205973-47207690	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:47205729-47209169	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:47205533-47207530	HepG2	liver:	n/a	n/a
12	MAZ	chr11:47206040-47209303	IMR90	lung:	n/a	chr11:47207005-47207015 chr11:47208870-47208880 chr11:47207105-47207115 chr11:47207475-47207485 chr11:47207774-47207784 chr11:47208558-47208565
13	MAX	chr11:47205912-47209210	HepG2	liver:	n/a	chr11:47207005-47207015 chr11:47208870-47208880 chr11:47207105-47207115 chr11:47207475-47207485 chr11:47207774-47207784 chr11:47208558-47208565

No.	Distal block	Cell Line	Cell type
1	chr11:47205835..47208468-chr11:47280225..47282817,2	MCF-7	breast:
2	chr11:47205640..47208812-chr11:47225906..47229370,3	MCF-7	breast:
3	chr11:47202119..47205492-chr11:47206060..47209673,5	K562	blood:
4	chr11:47204494..47207545-chr11:47289955..47292546,3	K562	blood:
5	chr11:47205635..47209843-chr11:47268961..47271979,7	MCF-7	breast:
6	chr11:47205217..47215436-chr11:47233934..47241095,26	MCF-7	breast:
7	chr11:47205613..47207687-chr11:47429461..47432184,2	K562	blood:
8	chr11:47205689..47216568-chr11:47232414..47239487,27	MCF-7	breast:
9	chr11:47205996..47209414-chr11:47263017..47267262,4	MCF-7	breast:
10	chr11:47204023..47207155-chr11:47207314..47211225,4	K562	blood:
11	chr11:47203683..47208496-chr11:47223862..47228000,5	MCF-7	breast:
12	chr11:47205341..47210329-chr11:47212095..47213798,5	MCF-7	breast:
13	chr11:47205837..47210171-chr11:47289770..47293955,7	MCF-7	breast:
14	chr11:47205592..47209017-chr11:47278399..47281373,5	MCF-7	breast:

Variant related genes	Relation type
PACSIN3	TF binding region
ENSG00000025434	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000243802	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000266540	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10466478	0.83[CHB][hapmap]
rs10501319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1055447	0.84[GIH][hapmap]
rs1060573	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs10742797	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769226	0.81[ASN][1000 genomes]
rs10769227	0.82[ASN][1000 genomes]
rs10769228	0.82[ASN][1000 genomes]
rs10769234	0.86[CHB][hapmap]
rs10769248	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838640	0.81[ASN][1000 genomes]
rs10838641	0.82[ASN][1000 genomes]
rs10838644	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.84[ASN][1000 genomes]
rs10838646	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10838652	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs10838658	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838660	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs10838662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838663	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10838664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039074	0.90[CHB][hapmap]
rs11039080	0.88[ASN][1000 genomes]
rs11039081	0.90[ASN][1000 genomes]
rs11039097	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039098	0.81[ASN][1000 genomes]
rs11039105	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039112	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039119	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs11600668	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs11601798	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603373	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12224096	0.82[CHB][hapmap]
rs12417519	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12574410	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12796744	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs1872896	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs2029298	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs2087215	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758666	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3758667	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3781619	0.82[CHD][hapmap]
rs3922684	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4269876	0.92[ASN][1000 genomes]
rs4315028	0.90[ASN][1000 genomes]
rs4494268	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4498951	0.92[ASN][1000 genomes]
rs4528282	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4548577	0.82[ASN][1000 genomes]
rs4567413	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs4576779	0.92[ASN][1000 genomes]
rs4587689	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4752951	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4752957	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs4752962	0.83[CHB][hapmap]
rs4752965	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4752967	0.83[CHB][hapmap]
rs4752968	0.86[ASN][1000 genomes]
rs4752969	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61896133	0.92[ASN][1000 genomes]
rs61896136	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61897787	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61897844	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61897857	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6485726	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs6485739	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7103581	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7108822	0.91[CEU][hapmap];0.87[ASN][1000 genomes]
rs7108902	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7111270	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7112854	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7114683	0.88[ASN][1000 genomes]
rs7121418	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7123632	0.81[ASN][1000 genomes]
rs7124648	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs7125807	0.82[CHB][hapmap];0.86[GIH][hapmap]
rs7126005	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs7127741	0.91[CEU][hapmap];0.88[ASN][1000 genomes]
rs7128650	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs7130006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747650	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7931260	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7935346	0.82[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs7937101	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs7940240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7945315	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7946709	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7950753	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs7951979	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901747	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923324	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv897324	chr11:47193566-47212032	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7937410	NUP160	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47197000-47207600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr11:47198800-47206400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47199600-47206600	Weak transcription	HUVEC	blood vessel
4	chr11:47199600-47206800	Weak transcription	Fetal Kidney	kidney
5	chr11:47199600-47207000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:47199800-47206200	Strong transcription	NHEK	skin
7	chr11:47199800-47206400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:47199800-47206400	Weak transcription	Osteobl	bone
9	chr11:47200000-47206200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:47200000-47206600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:47200000-47206600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:47200000-47207200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:47200200-47206400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:47200200-47206800	Weak transcription	Dnd41	blood
15	chr11:47200400-47207200	Weak transcription	K562	blood
16	chr11:47201600-47206400	Enhancers	Fetal Heart	heart
17	chr11:47202000-47206200	Weak transcription	A549	lung
18	chr11:47202400-47206200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:47202400-47206400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:47202400-47206400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:47202400-47206600	Weak transcription	Aorta	Aorta
22	chr11:47203000-47206200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:47203000-47206400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:47203800-47206200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:47204200-47206400	Enhancers	HSMMtube	muscle
26	chr11:47204800-47206200	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr11:47204800-47206400	Weak transcription	Ovary	ovary
28	chr11:47205000-47206200	Enhancers	Brain Cingulate Gyrus	brain
29	chr11:47205000-47206200	Enhancers	Brain Substantia Nigra	brain
30	chr11:47205000-47206200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
31	chr11:47205000-47206200	Enhancers	Gastric	stomach
32	chr11:47205000-47206200	Weak transcription	Right Atrium	heart
33	chr11:47205400-47206600	Enhancers	Spleen	Spleen
34	chr11:47205600-47206200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr11:47205600-47206200	Transcr. at gene 5' and 3'	Hela-S3	cervix
36	chr11:47205600-47206200	Genic enhancers	NHLF	lung
37	chr11:47205600-47206400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:47205600-47206600	Enhancers	NHDF-Ad	bronchial
39	chr11:47205600-47206800	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr11:47205600-47207000	Flanking Active TSS	Fetal Intestine Large	intestine
41	chr11:47205600-47207400	Flanking Active TSS	Liver	Liver
42	chr11:47205600-47208200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:47205600-47208200	Active TSS	Left Ventricle	heart
44	chr11:47205800-47206200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
45	chr11:47205800-47206200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:47205800-47206200	Enhancers	Pancreas	Pancrea
47	chr11:47205800-47206200	Enhancers	Placenta Amnion	Placenta Amnion
48	chr11:47205800-47206200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
49	chr11:47205800-47206400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:47205800-47206400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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