Variant report

Variant	rs10898880
Chromosome Location	chr11:72525111-72525112
allele	A/C
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	POU2F2	chr11:72524800-72525262	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:72523148-72527053	IMR90	lung:	n/a	n/a
3	POLR2A	chr11:72523665-72527030	GM12891	blood:	n/a	n/a
4	E2F4	chr11:72525007-72526202	MCF10A-Er-Src	breast:	n/a	chr11:72525472-72525483 chr11:72525451-72525462 chr11:72525349-72525357 chr11:72525349-72525357 chr11:72525348-72525358 chr11:72525393-72525402 chr11:72525350-72525357 chr11:72525159-72525168 chr11:72525384-72525394 chr11:72525383-72525392
5	POLR2A	chr11:72523591-72526356	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:72523701-72527157	HL-60	blood:	n/a	n/a
7	RELA	chr11:72523793-72527038	GM12891	blood:	n/a	n/a
8	POLR2A	chr11:72524710-72526238	HEK293	kidney:	n/a	n/a
9	SMC3	chr11:72523879-72526251	Hela-S3	cervix:	n/a	chr11:72525805-72525813 chr11:72525802-72525812 chr11:72525395-72525409 chr11:72525395-72525405
10	FOXM1	chr11:72523889-72525677	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr11:72524766-72525635	K562	blood:	n/a	n/a
12	TAF1	chr11:72524952-72525198	A549	lung:	n/a	n/a
13	HEY1	chr11:72524839-72525256	K562	blood:	n/a	n/a
14	NRF1	chr11:72524968-72525485	GM12878	blood:	n/a	chr11:72525389-72525398
15	HCFC1	chr11:72524808-72525647	K562	blood:	n/a	n/a
16	YY1	chr11:72524893-72525798	GM12891	blood:	n/a	chr11:72525383-72525392 chr11:72525383-72525394 chr11:72525061-72525075 chr11:72525387-72525401 chr11:72525624-72525643 chr11:72525386-72525395
17	POU2F2	chr11:72524837-72525202	GM12878	blood:	n/a	n/a
18	MAX	chr11:72523973-72526390	K562	blood:	n/a	chr11:72525182-72525191
19	FOXM1	chr11:72524147-72525566	GM12878	blood:	n/a	n/a
20	E2F6	chr11:72524642-72525257	A549	lung:	n/a	chr11:72525159-72525168
21	TAF1	chr11:72524812-72526245	Hela-S3	cervix:	n/a	n/a
22	CREB1	chr11:72524952-72526226	H1-hESC	embryonic stem cell:	n/a	n/a
23	CEBPB	chr11:72523927-72526134	Hela-S3	cervix:	n/a	n/a
24	ZMIZ1	chr11:72524831-72525826	K562	blood:	n/a	n/a
25	EP300	chr11:72524950-72526274	GM12878	blood:	n/a	chr11:72525057-72525073 chr11:72525389-72525398
26	EP300	chr11:72525000-72525629	K562	blood:	n/a	chr11:72525057-72525073 chr11:72525389-72525398
27	PAX5	chr11:72524902-72525900	GM12892	blood:	n/a	n/a
28	MAFK	chr11:72524001-72526043	Hela-S3	cervix:	n/a	n/a
29	YY1	chr11:72524787-72525133	H1-hESC	embryonic stem cell:	n/a	chr11:72525061-72525075
30	EP300	chr11:72524885-72525914	A549	lung:	n/a	chr11:72525057-72525073 chr11:72525389-72525398
31	MAZ	chr11:72523987-72526256	GM12878	blood:	n/a	chr11:72525182-72525191
32	BHLHE40	chr11:72524767-72525425	A549	lung:	n/a	chr11:72525026-72525042 chr11:72525385-72525401
33	CHD1	chr11:72523589-72526562	IMR90	lung:	n/a	chr11:72525660-72525670
34	ELK1	chr11:72524903-72525712	Hela-S3	cervix:	n/a	n/a
35	YY1	chr11:72523875-72526259	GM12878	blood:	n/a	chr11:72525383-72525392 chr11:72525383-72525394 chr11:72525061-72525075 chr11:72525387-72525401 chr11:72525624-72525643 chr11:72525386-72525395
36	PML	chr11:72524890-72525309	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:72524889-72525909	HepG2	liver:	n/a	n/a
38	CHD2	chr11:72523855-72526308	Hela-S3	cervix:	n/a	chr11:72525660-72525670
39	ZC3H11A	chr11:72524687-72525538	K562	blood:	n/a	n/a
40	RUNX3	chr11:72523901-72526528	GM12878	blood:	n/a	n/a
41	JUND	chr11:72525067-72525346	HepG2	liver:	n/a	n/a
42	MXI1	chr11:72523716-72526356	Hela-S3	cervix:	n/a	n/a
43	SP1	chr11:72524964-72526268	H1-hESC	embryonic stem cell:	n/a	chr11:72525758-72525770 chr11:72525426-72525435 chr11:72525758-72525770 chr11:72525157-72525169 chr11:72525157-72525169 chr11:72525426-72525435 chr11:72525391-72525403 chr11:72525393-72525402 chr11:72525159-72525168 chr11:72525425-72525437 chr11:72525425-72525437 chr11:72525391-72525403 chr11:72525158-72525167 chr11:72525427-72525436
44	REST	chr11:72523593-72525363	A549	lung:	n/a	chr11:72525027-72525040
45	POLR2A	chr11:72523753-72526402	GM12891	blood:	n/a	n/a
46	ZBTB7A	chr11:72524895-72525707	K562	blood:	n/a	n/a
47	YY1	chr11:72524769-72526220	HepG2	liver:	n/a	chr11:72525383-72525392 chr11:72525383-72525394 chr11:72525061-72525075 chr11:72525387-72525401 chr11:72525624-72525643 chr11:72525386-72525395
48	HDAC2	chr11:72524781-72525130	K562	blood:	n/a	n/a
49	BCL3	chr11:72524858-72525625	GM12878	blood:	n/a	chr11:72525377-72525386 chr11:72525385-72525394 chr11:72525383-72525396 chr11:72525124-72525133 chr11:72525386-72525399 chr11:72525119-72525132
50	RELA	chr11:72524423-72526984	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:72434436..72438940-chr11:72523674..72527576,8	MCF-7	breast:
2	chr11:72524393..72525198-chr5:141228453..141229185,2	Hela-S3	cervix:
3	chr11:72503176..72507418-chr11:72523751..72527635,5	MCF-7	breast:
4	chr11:72524589..72525262-chr6:42750251..42750753,2	Hela-S3	cervix:
5	chr11:72525050..72525778-chr6:36561890..36562542,2	Hela-S3	cervix:
6	chr11:72490395..72495168-chr11:72521187..72527739,13	MCF-7	breast:
7	chr11:72525068..72525975-chr17:7475724..7476658,2	Hela-S3	cervix:
8	chr11:72524994..72525910-chr19:12902178..12902779,2	Hela-S3	cervix:
9	chr11:72469058..72470946-chr11:72524668..72526420,2	MCF-7	breast:
10	chr11:72495938..72498335-chr11:72525039..72527037,2	MCF-7	breast:
11	chr11:72524384..72525147-chr5:14979898..14980796,2	Hela-S3	cervix:
12	chr11:72525018..72525976-chr6:17706298..17706931,2	Hela-S3	cervix:
13	chr11:72406538..72408722-chr11:72523842..72525455,2	MCF-7	breast:
14	chr11:72524343..72526457-chr11:76493236..76495527,2	MCF-7	breast:
15	chr1:225117334..225118220-chr11:72524845..72525840,2	Hela-S3	cervix:
16	chr11:72502078..72507217-chr11:72523813..72527208,9	K562	blood:
17	chr11:72524903..72525656-chr21:44299090..44299829,2	Hela-S3	cervix:
18	chr11:72524689..72525324-chr7:32534926..32535537,2	NB4	blood:
19	chr11:72435321..72438688-chr11:72524163..72527282,5	K562	blood:
20	chr11:72487526..72509577-chr11:72522325..72536312,93	MCF-7	breast:
21	chr1:28908038..28908570-chr11:72524680..72525648,2	Hela-S3	cervix:
22	chr11:72460411..72465058-chr11:72522153..72526935,8	MCF-7	breast:
23	chr11:72461703..72464740-chr11:72523811..72527033,4	K562	blood:
24	chr11:72502776..72504800-chr11:72523813..72526790,2	K562	blood:
25	chr11:72524629..72525134-chr11:72532680..72533221,2	Hela-S3	cervix:
26	chr1:144533506..144534133-chr11:72524969..72526154,3	Hela-S3	cervix:
27	chr11:72524882..72525386-chr17:25621000..25621905,2	Hela-S3	cervix:
28	chr11:72524854..72525550-chr7:45018514..45019297,2	Hela-S3	cervix:
29	chr11:72523752..72525675-chr11:72852917..72854760,2	K562	blood:
30	chr11:2906485..2907224-chr11:72524690..72525363,2	Hela-S3	cervix:
31	chr11:72524761..72525528-chr14:50052788..50053637,2	HCT-116	colon:
32	chr1:113932997..113933930-chr11:72525071..72525740,2	Hela-S3	cervix:
33	chr11:72524630..72525469-chr20:62168590..62169381,2	Hela-S3	cervix:
34	chr11:72524647..72525382-chr2:88315171..88316099,2	Hela-S3	cervix:
35	chr11:72468837..72471301-chr11:72524251..72525831,2	MCF-7	breast:
36	chr11:72524730..72525446-chr14:51297304..51298077,2	NB4	blood:
37	chr1:174968289..174969166-chr11:72524751..72525445,2	Hela-S3	cervix:
38	chr11:72432071..72434614-chr11:72523637..72525908,4	K562	blood:
39	chr11:72525059..72525949-chr7:2394495..2394995,2	NB4	blood:
40	chr11:72504451..72505136-chr11:72525016..72525872,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STARD10-1	chr11:72523491-72525129	NONHSAT022801

Variant related genes	Relation type
ATG16L2	TF binding region
ENSG00000129757	Chromatin interaction
ENSG00000137478	Chromatin interaction
ENSG00000168010	Chromatin interaction
ENSG00000136286	Chromatin interaction
ENSG00000081026	Chromatin interaction
ENSG00000105778	Chromatin interaction
ENSG00000197989	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000101213	Chromatin interaction
ENSG00000213741	Chromatin interaction
ENSG00000160194	Chromatin interaction
ENSG00000124789	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000106263	Chromatin interaction
ENSG00000186635	Chromatin interaction
ENSG00000185842	Chromatin interaction
ENSG00000263583	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000265064	Chromatin interaction
ENSG00000160193	Chromatin interaction
ENSG00000100503	Chromatin interaction
ENSG00000258486	Chromatin interaction
ENSG00000161960	Chromatin interaction
ENSG00000214530	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000272269	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000109046	Chromatin interaction
ENSG00000182704	Chromatin interaction
ENSG00000255100	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1000620	0.95[CEU][hapmap];0.88[CHD][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10431171	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10431172	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10431174	0.87[AMR][1000 genomes]
rs10751213	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10751215	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10751216	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10898877	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10898879	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10898881	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs11235592	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11235594	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHD][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11235596	1.00[CEU][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1864653	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1975109	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35343925	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35668754	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35752694	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4459331	0.91[CEU][hapmap];0.88[CHD][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4459332	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs485099	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4944796	0.95[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4944797	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4944800	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4944802	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4944805	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6592486	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6592489	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6592490	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs677231	0.95[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7110719	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7952617	0.95[AMR][1000 genomes];0.92[EUR][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	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10898880	STARD10	cis	cerebellum	SCAN
rs10898880	ARHGEF17	cis	cerebellum	SCAN
rs10898880	FGF4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72523000-72525200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:72523200-72527200	Active TSS	Primary monocytes fromperipheralblood	blood
3	chr11:72523600-72525200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr11:72523600-72525200	Flanking Active TSS	HMEC	breast
5	chr11:72523600-72526400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr11:72523600-72526800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr11:72523600-72527000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:72523800-72525200	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr11:72523800-72525200	Flanking Active TSS	K562	blood
10	chr11:72523800-72526000	Active TSS	Thymus	Thymus
11	chr11:72523800-72526200	Active TSS	Aorta	Aorta
12	chr11:72524000-72525800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:72524200-72526400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:72524200-72526600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr11:72524200-72526800	Active TSS	Small Intestine	intestine
16	chr11:72524400-72525200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr11:72524400-72526000	Active TSS	A549	lung
18	chr11:72524400-72526200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr11:72524400-72526200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:72524400-72526400	Active TSS	Fetal Kidney	kidney
21	chr11:72524400-72526400	Active TSS	Ovary	ovary
22	chr11:72524400-72526600	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr11:72524400-72527200	Active TSS	GM12878-XiMat	blood
24	chr11:72524600-72525800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:72524600-72525800	Active TSS	Placenta Amnion	Placenta Amnion
26	chr11:72524600-72526000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr11:72524600-72526000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:72524600-72526000	Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr11:72524600-72526000	Active TSS	Brain Angular Gyrus	brain
30	chr11:72524600-72526000	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr11:72524600-72526000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:72524600-72526200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:72524600-72526200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:72524600-72526200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:72524600-72526200	Active TSS	Brain Anterior Caudate	brain
36	chr11:72524600-72526200	Active TSS	Colon Smooth Muscle	Colon
37	chr11:72524600-72526200	Active TSS	Left Ventricle	heart
38	chr11:72524600-72526200	Active TSS	NHDF-Ad	bronchial
39	chr11:72524600-72526400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:72524600-72526400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr11:72524600-72526600	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr11:72524600-72526600	Active TSS	Psoas Muscle	Psoas
43	chr11:72524600-72526800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr11:72524600-72527200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:72524600-72527200	Active TSS	Monocytes-CD14+_RO01746	blood
46	chr11:72524800-72525200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:72524800-72525200	Flanking Active TSS	HSMM	muscle
48	chr11:72524800-72525600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:72524800-72525600	Active TSS	Fetal Brain Female	brain
50	chr11:72524800-72525800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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