Variant report

Variant	rs11825542
Chromosome Location	chr11:9481875-9481876
allele	C/T
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	chr11:9480308-9483702	PFSK-1	brain:	n/a	n/a
2	GABPA	chr11:9481820-9482843	A549	lung:	n/a	n/a
3	MXI1	chr11:9481736-9483787	Hela-S3	cervix:	n/a	chr11:9481818-9481833
4	REST	chr11:9481845-9482312	A549	lung:	n/a	n/a
5	YY1	chr11:9481839-9482860	A549	lung:	n/a	chr11:9482220-9482242 chr11:9482686-9482700 chr11:9482769-9482783 chr11:9482689-9482703 chr11:9482671-9482680 chr11:9482689-9482698 chr11:9482534-9482548 chr11:9482686-9482695 chr11:9482672-9482686 chr11:9482231-9482239
6	TAF1	chr11:9481378-9483190	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:9480817-9484127	GM18505	blood:	n/a	n/a
8	CREB1	chr11:9481658-9483195	HepG2	liver:	n/a	chr11:9482392-9482405
9	CHD2	chr11:9481133-9483012	K562	blood:	n/a	chr11:9482147-9482157
10	POLR2A	chr11:9481759-9482286	A549	lung:	n/a	n/a
11	TCF12	chr11:9481756-9483231	ECC-1	luminal epithelium:	n/a	n/a
12	SP1	chr11:9481262-9483289	HCT-116	colon:	n/a	chr11:9482284-9482293 chr11:9482494-9482515 chr11:9482368-9482377 chr11:9482511-9482520 chr11:9482509-9482521 chr11:9482366-9482377 chr11:9482450-9482471 chr11:9482510-9482519 chr11:9482509-9482521
13	YY1	chr11:9481712-9483071	SK-N-SH_RA	brain:	n/a	chr11:9482220-9482242 chr11:9482686-9482700 chr11:9482769-9482783 chr11:9482689-9482703 chr11:9482671-9482680 chr11:9482689-9482698 chr11:9482534-9482548 chr11:9482686-9482695 chr11:9482672-9482686 chr11:9482231-9482239
14	POLR2A	chr11:9480875-9483890	U87	brain:	n/a	n/a
15	POLR2A	chr11:9481042-9483691	HL-60	blood:	n/a	n/a
16	YY1	chr11:9481637-9483140	A549	lung:	n/a	chr11:9482220-9482242 chr11:9482686-9482700 chr11:9482769-9482783 chr11:9482689-9482703 chr11:9482671-9482680 chr11:9483065-9483076 chr11:9482689-9482698 chr11:9482534-9482548 chr11:9482686-9482695 chr11:9482672-9482686 chr11:9482231-9482239
17	TEAD4	chr11:9481277-9483422	K562	blood:	n/a	n/a
18	SP1	chr11:9481651-9483453	A549	lung:	n/a	chr11:9482284-9482293 chr11:9482494-9482515 chr11:9482368-9482377 chr11:9482511-9482520 chr11:9482509-9482521 chr11:9482366-9482377 chr11:9482450-9482471 chr11:9482510-9482519 chr11:9482509-9482521
19	NFIC	chr11:9481586-9482416	ECC-1	luminal epithelium:	n/a	n/a
20	TBP	chr11:9481249-9483906	Hela-S3	cervix:	n/a	n/a
21	TAF1	chr11:9481756-9483239	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr11:9481690-9483171	GM12878	blood:	n/a	n/a
23	FOXM1	chr11:9481183-9483652	GM12878	blood:	n/a	n/a
24	FOXM1	chr11:9481865-9482990	ECC-1	luminal epithelium:	n/a	n/a
25	MYC	chr11:9481875-9482734	MCF-7	breast:	n/a	n/a
26	SP1	chr11:9481807-9482941	H1-hESC	embryonic stem cell:	n/a	chr11:9482284-9482293 chr11:9482494-9482515 chr11:9482368-9482377 chr11:9482511-9482520 chr11:9482509-9482521 chr11:9482366-9482377 chr11:9482450-9482471 chr11:9482510-9482519 chr11:9482509-9482521
27	MYC	chr11:9481846-9483177	Hela-S3	cervix:	n/a	n/a
28	TAF1	chr11:9481727-9483142	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr11:9481141-9483836	GM18951	blood:	n/a	n/a
30	TAF1	chr11:9481273-9482320	SK-N-SH	brain:	n/a	n/a
31	MXI1	chr11:9481565-9483184	HepG2	liver:	n/a	chr11:9481818-9481833
32	HEY1	chr11:9481793-9482337	K562	blood:	n/a	n/a
33	POLR2A	chr11:9481796-9482322	HepG2	liver:	n/a	n/a
34	TBL1XR1	chr11:9481171-9483236	GM12878	blood:	n/a	n/a
35	HEY1	chr11:9481012-9482322	HepG2	liver:	n/a	n/a
36	POLR2A	chr11:9480878-9483810	HCT-116	colon:	n/a	n/a
37	REST	chr11:9481681-9482348	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr11:9481144-9483699	ProgFib	skin:	n/a	n/a
39	MYC	chr11:9481383-9483217	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF7	chr11:9481725-9482314	H1-hESC	embryonic stem cell:	n/a	n/a
41	IRF4	chr11:9481869-9482470	GM12878	blood:	n/a	n/a
42	ATF2	chr11:9481264-9483210	GM12878	blood:	n/a	chr11:9482393-9482404
43	ZMIZ1	chr11:9481617-9483147	K562	blood:	n/a	n/a
44	YY1	chr11:9481707-9483062	H1-hESC	embryonic stem cell:	n/a	chr11:9482220-9482242 chr11:9482686-9482700 chr11:9482769-9482783 chr11:9482689-9482703 chr11:9482671-9482680 chr11:9482689-9482698 chr11:9482534-9482548 chr11:9482686-9482695 chr11:9482672-9482686 chr11:9482231-9482239
45	POLR2A	chr11:9481846-9482426	K562	blood:	n/a	n/a
46	POLR2A	chr11:9480642-9483619	K562	blood:	n/a	n/a
47	MAX	chr11:9481629-9483193	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr11:9480568-9483216	ECC-1	luminal epithelium:	n/a	n/a
49	TAF7	chr11:9481619-9483262	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr11:9481820-9481970	SK-N-SH_RA	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:9481875-9481925	HepG2	liver:	n/a
2	chr11:9481875-9481925	PANC-1	pancreas:	n/a
3	chr11:9481875-9481925	HAEpiC	amniotic membrane:	n/a
4	chr11:9481875-9481925	T-47D	breast:	n/a
5	chr11:9481875-9481925	NH-A	brain:	n/a
6	chr11:9481875-9481925	HCT-116	colon:	n/a
7	chr11:9481875-9481925	HNPCEpiC	eye:	n/a
8	chr11:9481875-9481925	BJ	skin:	n/a
9	chr11:9481875-9481925	NT2-D1	testis:	n/a
10	chr11:9481875-9481925	CMK	blood:	n/a
11	chr11:9481875-9481925	NHDF-neo	bronchial:	n/a
12	chr11:9481875-9481925	GM12891	blood:	n/a
13	chr11:9481875-9481925	ovcar-3	ovarian:	n/a
14	chr11:9481875-9481925	IMR90	lung:	fetal
15	chr11:9481875-9481925	SAEC	small airway:	n/a
16	chr11:9481875-9481925	RPTEC	kidney:	n/a
17	chr11:9481875-9481925	AG04449	skin:	fetal
18	chr11:9481875-9481925	Caco-2	colon:	n/a
19	chr11:9481875-9481925	Hela-S3	cervix:	n/a
20	chr11:9481875-9481925	AG09309	skin:	n/a
21	chr11:9481875-9481925	LNCaP	prostate:	n/a
22	chr11:9481875-9481925	NB4	blood:	n/a
23	chr11:9481875-9481925	GM19239	blood:	n/a
24	chr11:9481875-9481925	HRPEpiC	eye:	n/a
25	chr11:9481875-9481925	HRE	kidney:	n/a
26	chr11:9481875-9481925	HUVEC	blood vessel:	n/a
27	chr11:9481875-9481925	HCF	heart:	n/a
28	chr11:9481875-9481925	MCF-7	breast:	n/a
29	chr11:9481875-9481925	BE2_C	brain:	n/a
30	chr11:9481875-9481925	A549	lung:	n/a
31	chr11:9481875-9481925	NHBE	bronchial:	n/a
32	chr11:9481875-9481925	PrEC	prostate:	n/a
33	chr11:9481875-9481925	ProgFib	skin:	n/a
34	chr11:9481875-9481925	AoSMC	blood vessel:	n/a
35	chr11:9481875-9481925	HEK293	kidney:	embryo
36	chr11:9481875-9481925	HMEC	breast:	n/a
37	chr11:9481875-9481925	HCM	heart:	n/a
38	chr11:9481875-9481925	AG04450	lung:	fetal
39	chr11:9481875-9481925	GM12878	blood:	n/a
40	chr11:9481875-9481925	SK-N-SH_RA	brain:	n/a
41	chr11:9481875-9481925	H1-hESC	embryonic stem cell:	embryo
42	chr11:9481875-9481925	PFSK-1	brain:	n/a
43	chr11:9481875-9481925	SK-N-MC	brain:	n/a
44	chr11:9481875-9481925	MCF10A-Er-Src	breast:	n/a
45	chr11:9481875-9481925	GM06990	blood:	n/a
46	chr11:9481875-9481925	HCPEpiC	choroid plexus:	n/a
47	chr11:9481875-9481925	GM12892	blood:	n/a
48	chr11:9481875-9481925	K562	blood:	n/a
49	chr11:9481875-9481925	SKMC	muscle:	n/a
50	chr11:9481875-9481925	HEEpiC	esophagus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9481508..9485106-chr11:9595203..9601095,6	MCF-7	breast:
2	chr11:9480226..9484903-chr11:9591788..9598525,12	MCF-7	breast:
3	chr11:9481580..9482474-chr17:7387306..7388177,3	Hela-S3	cervix:
4	chr11:9333668..9337804-chr11:9478729..9484496,11	K562	blood:
5	chr11:9447701..9450572-chr11:9481621..9483172,2	MCF-7	breast:
6	chr11:9444949..9446836-chr11:9480853..9482944,2	K562	blood:
7	chr11:9481791..9482882-chr7:25164334..25165288,3	Hela-S3	cervix:
8	chr11:9481080..9484532-chr11:9545856..9548015,3	MCF-7	breast:
9	chr11:9285385..9287169-chr11:9480610..9482898,2	K562	blood:
10	chr11:9478618..9485582-chr11:9593299..9599536,13	K562	blood:
11	chr11:9481806..9482317-chr3:57583282..57583911,2	Hela-S3	cervix:
12	chr11:9285399..9287969-chr11:9480073..9484247,5	MCF-7	breast:
13	chr11:9481690..9482581-chr20:30194519..30195290,2	Hela-S3	cervix:
14	chr11:9481642..9483596-chr11:9779160..9782132,2	K562	blood:
15	chr11:9284942..9289829-chr11:9481407..9484206,5	MCF-7	breast:
16	chr11:9429811..9433973-chr11:9481355..9484368,4	MCF-7	breast:
17	chr11:9481490..9482152-chr11:62608638..62609549,2	NB4	blood:
18	chr11:9405101..9410331-chr11:9478772..9485340,14	K562	blood:
19	chr11:9479692..9486524-chr11:9491765..9498081,14	K562	blood:
20	chr11:9334187..9337944-chr11:9481178..9484496,6	K562	blood:
21	chr11:9479099..9485582-chr11:9593306..9599058,18	K562	blood:
22	chr11:9403958..9411793-chr11:9477944..9485616,22	K562	blood:
23	chr11:9479980..9482925-chr11:9627285..9628824,2	MCF-7	breast:
24	chr11:9481460..9483596-chr11:9780067..9782132,2	K562	blood:
25	chr11:9481559..9482413-chr12:58165702..58166309,2	Hela-S3	cervix:
26	chr11:9481705..9482469-chr3:23987267..23987797,2	Hela-S3	cervix:
27	chr11:9285208..9288330-chr11:9480610..9483327,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM41B-5	chr11:9481103-9482245	NONHSAT017922

Variant related genes	Relation type
ZNF143	TF binding region
ZNF143	CpG island
ENSG00000181222	Chromatin interaction
ENSG00000245522	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000243964	Chromatin interaction
ENSG00000172115	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000272146	Chromatin interaction
ENSG00000205339	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000246273	Chromatin interaction
ENSG00000201998	Chromatin interaction
ENSG00000184014	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000166471	Chromatin interaction
ENSG00000166483	Chromatin interaction
ENSG00000238387	Chromatin interaction
ENSG00000123427	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11823865	1.00[EUR][1000 genomes]
rs11824009	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1865560	1.00[EUR][1000 genomes]
rs34831554	1.00[EUR][1000 genomes]
rs4328248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4414214	1.00[AMR][1000 genomes]
rs4910057	1.00[EUR][1000 genomes]
rs57760683	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58608279	1.00[EUR][1000 genomes]
rs59206639	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59403069	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59432040	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60199973	1.00[EUR][1000 genomes]
rs60748041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61003414	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61708669	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7107607	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7113100	1.00[EUR][1000 genomes]
rs7115224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7115556	0.83[AFR][1000 genomes]
rs7119701	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73408245	1.00[EUR][1000 genomes]
rs73408270	1.00[EUR][1000 genomes]
rs73408291	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9480600-9483800	Active TSS	Placenta	Placenta
2	chr11:9480600-9484000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr11:9480800-9482800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:9480800-9483200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:9480800-9483400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:9480800-9483400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr11:9480800-9483400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:9480800-9483400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:9480800-9483400	Active TSS	Brain Cingulate Gyrus	brain
10	chr11:9480800-9483400	Active TSS	Rectal Smooth Muscle	rectum
11	chr11:9480800-9483400	Active TSS	HMEC	breast
12	chr11:9480800-9483400	Active TSS	NHEK	skin
13	chr11:9480800-9483600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:9480800-9483600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:9480800-9483600	Active TSS	Esophagus	oesophagus
16	chr11:9480800-9483600	Active TSS	Pancreas	Pancrea
17	chr11:9480800-9483800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:9480800-9483800	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr11:9480800-9483800	Active TSS	GM12878-XiMat	blood
20	chr11:9480800-9484000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:9480800-9484000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:9480800-9484000	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr11:9480800-9484000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:9480800-9484000	Active TSS	Fetal Brain Female	brain
25	chr11:9480800-9484000	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr11:9480800-9484200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr11:9480800-9484200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr11:9480800-9484200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr11:9480800-9484200	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr11:9480800-9484200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:9480800-9484200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:9480800-9484200	Active TSS	HSMM	muscle
33	chr11:9481000-9482000	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr11:9481000-9482000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr11:9481000-9482200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr11:9481000-9483000	Active TSS	Primary hematopoietic stem cells	blood
37	chr11:9481000-9483200	Active TSS	Primary T cells from cord blood	blood
38	chr11:9481000-9483200	Active TSS	NH-A	brain
39	chr11:9481000-9483400	Active TSS	Brain Angular Gyrus	brain
40	chr11:9481000-9483400	Active TSS	Brain Anterior Caudate	brain
41	chr11:9481000-9483400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:9481000-9483400	Active TSS	Fetal Kidney	kidney
43	chr11:9481000-9483400	Active TSS	Stomach Smooth Muscle	stomach
44	chr11:9481000-9483400	Active TSS	A549	lung
45	chr11:9481000-9483600	Active TSS	Liver	Liver
46	chr11:9481000-9483600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr11:9481000-9483600	Active TSS	Fetal Stomach	stomach
48	chr11:9481000-9483600	Active TSS	Left Ventricle	heart
49	chr11:9481000-9483600	Active TSS	NHDF-Ad	bronchial
50	chr11:9481000-9483800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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