Variant report

Variant	rs11211030
Chromosome Location	chr1:45205323-45205324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:447)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:447 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr1:45205164-45205723	K562	blood:	n/a	n/a
2	IRF1	chr1:45204852-45205726	K562	blood:	n/a	chr1:45205357-45205371 chr1:45205457-45205471
3	SIN3AK20	chr1:45205103-45205745	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45204789-45206347	K562	blood:	n/a	n/a
5	ELF1	chr1:45205013-45205803	MCF-7	breast:	n/a	chr1:45205449-45205458
6	TBP	chr1:45204957-45206190	K562	blood:	n/a	n/a
7	BCL3	chr1:45205101-45205722	A549	lung:	n/a	chr1:45205286-45205295
8	POLR2A	chr1:45205056-45205866	K562	blood:	n/a	n/a
9	CTCF	chr1:45205267-45205463	Lung_OC	lung:	n/a	n/a
10	NFIC	chr1:45204907-45205751	GM12878	blood:	n/a	n/a
11	FOXM1	chr1:45205132-45206050	SK-N-SH	brain:	n/a	n/a
12	PAX5	chr1:45205055-45205661	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:45205172-45206070	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOS	chr1:45204790-45205593	MCF10A-Er-Src	breast:	n/a	n/a
15	CREB1	chr1:45204958-45205840	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAFK	chr1:45205315-45205509	HepG2	liver:	n/a	n/a
17	CREB1	chr1:45204961-45206017	HepG2	liver:	n/a	n/a
18	ELK1	chr1:45204938-45205684	K562	blood:	n/a	n/a
19	NRF1	chr1:45204914-45206146	SK-N-SH	brain:	n/a	chr1:45205489-45205500
20	POLR2A	chr1:45204879-45205810	HCT-116	colon:	n/a	n/a
21	SP1	chr1:45205100-45205736	H1-hESC	embryonic stem cell:	n/a	chr1:45205457-45205468 chr1:45205458-45205467 chr1:45205358-45205368 chr1:45205358-45205368 chr1:45205457-45205469
22	NFIC	chr1:45204774-45205709	GM12878	blood:	n/a	n/a
23	TAF1	chr1:45205001-45205762	PFSK-1	brain:	n/a	n/a
24	MAZ	chr1:45205049-45205891	K562	blood:	n/a	n/a
25	TCF12	chr1:45204949-45205886	ECC-1	luminal epithelium:	n/a	n/a
26	E2F6	chr1:45205020-45205739	K562	blood:	n/a	n/a
27	HDAC2	chr1:45205067-45205582	K562	blood:	n/a	n/a
28	POLR2A	chr1:45204988-45205694	HUVEC	blood vessel:	n/a	n/a
29	GABPA	chr1:45205025-45205742	MCF-7	breast:	n/a	n/a
30	MAX	chr1:45204844-45205875	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:45204921-45206119	GM19099	blood:	n/a	n/a
32	POU2F2	chr1:45205068-45205701	GM12891	blood:	n/a	n/a
33	USF2	chr1:45205123-45205540	GM12878	blood:	n/a	n/a
34	BRCA1	chr1:45205089-45205611	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:45204680-45206288	SK-N-MC	brain:	n/a	n/a
36	SIN3AK20	chr1:45205231-45206075	H1-hESC	embryonic stem cell:	n/a	n/a
37	SRF	chr1:45205225-45205512	GM12878	blood:	n/a	chr1:45205293-45205311
38	TBP	chr1:45205008-45205733	HepG2	liver:	n/a	n/a
39	E2F6	chr1:45205204-45205735	H1-hESC	embryonic stem cell:	n/a	n/a
40	GTF2F1	chr1:45205025-45205692	K562	blood:	n/a	n/a
41	TAF1	chr1:45205097-45205653	Hela-S3	cervix:	n/a	n/a
42	BHLHE40	chr1:45205112-45205793	GM12878	blood:	n/a	n/a
43	STAT3	chr1:45205090-45205547	MCF10A-Er-Src	breast:	n/a	chr1:45205337-45205345
44	POLR2A	chr1:45205077-45205712	MCF10A-Er-Src	breast:	n/a	n/a
45	EP300	chr1:45205195-45205767	A549	lung:	n/a	n/a
46	MAX	chr1:45204949-45205971	SK-N-SH	brain:	n/a	n/a
47	ZBTB7A	chr1:45205143-45205737	K562	blood:	n/a	n/a
48	CBX3	chr1:45204809-45205685	K562	blood:	n/a	n/a
49	YY1	chr1:45205172-45205507	HepG2	liver:	n/a	chr1:45205436-45205450
50	MXI1	chr1:45205059-45205833	K562	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45204937..45205829-chr10:121632304..121633151,2	HCT-116	colon:
2	chr1:45205289..45206129-chr14:50234525..50235369,2	Hela-S3	cervix:
3	chr1:45203367..45205545-chr1:45283633..45285875,3	MCF-7	breast:
4	chr1:45185270..45188395-chr1:45203453..45205490,5	MCF-7	breast:
5	chr1:45204980..45205724-chr1:228270199..228270919,2	Hela-S3	cervix:
6	chr1:45205047..45205558-chr1:155278215..155279112,2	Hela-S3	cervix:
7	chr1:45204972..45205714-chr14:94547211..94548102,2	Hela-S3	cervix:
8	chr1:45205245..45207359-chr1:45265556..45268016,2	MCF-7	breast:
9	chr1:45203850..45207286-chr1:45238882..45241584,6	MCF-7	breast:
10	chr1:45203441..45205480-chr1:45305972..45309901,3	K562	blood:
11	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
12	chr1:45202642..45205441-chr1:45208047..45209564,2	MCF-7	breast:
13	chr1:45205081..45206794-chr1:45478593..45481166,2	K562	blood:
14	chr1:45204918..45205418-chr11:75945782..75946374,2	NB4	blood:
15	chr1:45204996..45206772-chr1:45226218..45229043,2	MCF-7	breast:
16	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
17	chr1:45193557..45198509-chr1:45202622..45207012,16	MCF-7	breast:
18	chr1:45204011..45207083-chr1:45240823..45243671,4	MCF-7	breast:
19	chr1:45205006..45205720-chr14:45430584..45431145,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
KIF2C	TF binding region
ENSG00000226499	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000089737	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000165516	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000197771	Chromatin interaction
ENSG00000160752	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000165948	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000179454	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10127448	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10465818	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211027	0.81[AMR][1000 genomes]
rs11211031	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211034	0.88[ASN][1000 genomes]
rs11211037	0.84[MEX][hapmap]
rs11211046	0.81[GIH][hapmap]
rs11584031	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11801067	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808189	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12059964	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs12094028	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12117881	0.83[ASN][1000 genomes]
rs12136048	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12136099	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12410588	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12732939	0.83[YRI][hapmap]
rs12742914	0.88[ASN][1000 genomes]
rs12746270	0.83[YRI][hapmap]
rs16832228	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263986	0.81[JPT][hapmap]
rs3795720	0.81[GIH][hapmap]
rs3820586	0.83[YRI][hapmap]
rs4542248	0.93[EUR][1000 genomes]
rs6429548	0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes]
rs6656337	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6658470	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6666987	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671255	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678729	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685176	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688710	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6689911	0.83[YRI][hapmap]
rs6693615	0.80[EUR][1000 genomes]
rs7512710	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518836	0.91[ASN][1000 genomes]
rs7524446	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7525308	0.88[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs7534487	0.83[YRI][hapmap]
rs7536146	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7550170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7555065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
7	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
8	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
9	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11211030	C1orf84	cis	parietal	SCAN
rs11211030	EIF2B3	cis	cerebellum	SCAN
rs11211030	SNORD38B	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45203800-45205600	Active TSS	Right Ventricle	heart
2	chr1:45203800-45205800	Active TSS	Thymus	Thymus
3	chr1:45203800-45206400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:45203800-45206600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:45204000-45205400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:45204000-45206200	Active TSS	Esophagus	oesophagus
7	chr1:45204200-45205400	Active TSS	Primary T cells fromperipheralblood	blood
8	chr1:45204200-45205400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:45204200-45205600	Active TSS	Colon Smooth Muscle	Colon
10	chr1:45204200-45205600	Active TSS	Fetal Thymus	thymus
11	chr1:45204200-45205600	Active TSS	Psoas Muscle	Psoas
12	chr1:45204200-45205800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:45204600-45205400	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr1:45204800-45205400	Active TSS	Liver	Liver
15	chr1:45204800-45205600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:45204800-45205600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:45204800-45205600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:45204800-45205600	Active TSS	Aorta	Aorta
19	chr1:45204800-45205600	Active TSS	Brain Angular Gyrus	brain
20	chr1:45204800-45205600	Active TSS	Brain Anterior Caudate	brain
21	chr1:45204800-45205600	Active TSS	Brain Cingulate Gyrus	brain
22	chr1:45204800-45205600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:45204800-45205600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:45204800-45205600	Active TSS	Brain Substantia Nigra	brain
25	chr1:45204800-45205600	Active TSS	Colonic Mucosa	Colon
26	chr1:45204800-45205600	Active TSS	Fetal Brain Male	brain
27	chr1:45204800-45205600	Active TSS	Fetal Brain Female	brain
28	chr1:45204800-45205600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr1:45204800-45205600	Active TSS	Fetal Muscle Trunk	muscle
30	chr1:45204800-45205600	Active TSS	Fetal Muscle Leg	muscle
31	chr1:45204800-45205600	Active TSS	Fetal Stomach	stomach
32	chr1:45204800-45205600	Active TSS	Rectal Smooth Muscle	rectum
33	chr1:45204800-45205800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:45204800-45205800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
35	chr1:45204800-45206000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr1:45204800-45206000	Active TSS	HSMMtube	muscle
37	chr1:45204800-45206000	Active TSS	NH-A	brain
38	chr1:45204800-45206000	Active TSS	NHDF-Ad	bronchial
39	chr1:45204800-45206200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr1:45204800-45206200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr1:45204800-45206200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:45204800-45206200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr1:45204800-45206200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:45204800-45206400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr1:45204800-45206400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:45204800-45206400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:45204800-45206400	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr1:45204800-45206400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:45204800-45206400	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:45204800-45206400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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