Variant report

Variant	rs677231
Chromosome Location	chr11:72504848-72504849
allele	A/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	YY1	chr11:72504735-72505388	K562	blood:	n/a	n/a
2	ZNF143	chr11:72504541-72505446	H1-hESC	embryonic stem cell:	n/a	chr11:72505139-72505148 chr11:72505141-72505150 chr11:72505241-72505259 chr11:72505190-72505199 chr11:72505132-72505150
3	SIN3AK20	chr11:72504777-72505349	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOS	chr11:72504489-72505318	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr11:72504800-72504950	AG04449	skin:	n/a	chr11:72504869-72504879 chr11:72504868-72504881 chr11:72504868-72504881 chr11:72504866-72504884 chr11:72504872-72504881 chr11:72504867-72504883 chr11:72504861-72504882
6	CTCF	chr11:72504629-72505079	GM20000	blood:	n/a	chr11:72504869-72504879 chr11:72504868-72504881 chr11:72504868-72504881 chr11:72504866-72504884 chr11:72504872-72504881 chr11:72504867-72504883 chr11:72504861-72504882
7	FOS	chr11:72504409-72505270	HUVEC	blood vessel:	n/a	n/a
8	HCFC1	chr11:72504381-72505706	K562	blood:	n/a	n/a
9	POLR2A	chr11:72504596-72505359	GM18951	blood:	n/a	n/a
10	POLR2A	chr11:72504753-72505174	U87	brain:	n/a	n/a
11	ATF3	chr11:72504272-72505184	A549	lung:	n/a	n/a
12	CEBPB	chr11:72504669-72505356	HepG2	liver:	n/a	n/a
13	SMARCB1	chr11:72504599-72505596	Hela-S3	cervix:	n/a	chr11:72505190-72505199 chr11:72505141-72505150
14	YY1	chr11:72504651-72505278	HCT-116	colon:	n/a	n/a
15	POLR2A	chr11:72504638-72505286	ECC-1	luminal epithelium:	n/a	n/a
16	TAF1	chr11:72504662-72505441	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr11:72504800-72504950	GM12875	blood:	n/a	chr11:72504869-72504879 chr11:72504868-72504881 chr11:72504868-72504881 chr11:72504866-72504884 chr11:72504872-72504881 chr11:72504867-72504883 chr11:72504861-72504882
18	MTA3	chr11:72504279-72505348	GM12878	blood:	n/a	n/a
19	MAZ	chr11:72504388-72505080	HepG2	liver:	n/a	chr11:72504718-72504727 chr11:72505055-72505064 chr11:72505058-72505065
20	POLR2A	chr11:72504670-72505190	U87	brain:	n/a	n/a
21	MYC	chr11:72504330-72505338	K562	blood:	n/a	chr11:72504718-72504727 chr11:72505055-72505064 chr11:72505058-72505065
22	USF1	chr11:72504516-72504937	A549	lung:	n/a	chr11:72504719-72504730
23	STAT5A	chr11:72504322-72505362	GM12878	blood:	n/a	chr11:72504554-72504561
24	RCOR1	chr11:72504470-72505281	HepG2	liver:	n/a	n/a
25	SMC3	chr11:72503960-72505558	SK-N-SH	brain:	n/a	chr11:72504868-72504882
26	POLR2A	chr11:72504528-72505346	HL-60	blood:	n/a	n/a
27	POLR2A	chr11:72504532-72505293	GM15510	blood:	n/a	n/a
28	CTCF	chr11:72504840-72504990	HEK293	kidney:	n/a	chr11:72504869-72504879 chr11:72504868-72504881 chr11:72504868-72504881 chr11:72504866-72504884 chr11:72504872-72504881 chr11:72504867-72504883 chr11:72504861-72504882
29	TEAD4	chr11:72504729-72505397	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr11:72504503-72504999	ECC-1	luminal epithelium:	n/a	chr11:72504864-72504883
31	CTCF	chr11:72504820-72504970	GM12874	blood:	n/a	chr11:72504869-72504879 chr11:72504868-72504881 chr11:72504868-72504881 chr11:72504866-72504884 chr11:72504872-72504881 chr11:72504867-72504883 chr11:72504861-72504882
32	POLR2A	chr11:72504527-72505378	Hela-S3	cervix:	n/a	n/a
33	MAFK	chr11:72504476-72505263	K562	blood:	n/a	n/a
34	RAD21	chr11:72504323-72505323	MCF-7	breast:	n/a	chr11:72504864-72504883 chr11:72505061-72505075
35	CTCF	chr11:72504529-72505030	H1-hESC	embryonic stem cell:	n/a	chr11:72504869-72504879 chr11:72504868-72504881 chr11:72504868-72504881 chr11:72504866-72504884 chr11:72504872-72504881 chr11:72504867-72504883 chr11:72504861-72504882
36	TAF1	chr11:72504727-72505293	H1-hESC	embryonic stem cell:	n/a	n/a
37	RELA	chr11:72504383-72505426	GM12878	blood:	n/a	n/a
38	BRCA1	chr11:72504612-72505276	HepG2	liver:	n/a	n/a
39	POLR2A	chr11:72504597-72505382	HCT-116	colon:	n/a	n/a
40	TCF3	chr11:72504774-72505112	GM12878	blood:	n/a	n/a
41	CTCF	chr11:72504820-72504970	AG09309	skin:	n/a	chr11:72504869-72504879 chr11:72504868-72504881 chr11:72504868-72504881 chr11:72504866-72504884 chr11:72504872-72504881 chr11:72504867-72504883 chr11:72504861-72504882
42	HEY1	chr11:72504434-72505417	HepG2	liver:	n/a	n/a
43	MYC	chr11:72504734-72504898	K562	blood:	n/a	n/a
44	USF1	chr11:72504493-72504906	H1-hESC	embryonic stem cell:	n/a	chr11:72504719-72504730
45	CHD2	chr11:72504512-72505359	GM12878	blood:	n/a	n/a
46	SP1	chr11:72504609-72505302	GM12878	blood:	n/a	chr11:72504858-72504872 chr11:72504865-72504879 chr11:72504866-72504875 chr11:72504864-72504876 chr11:72504864-72504876
47	GTF2F1	chr11:72504639-72505208	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF7L2	chr11:72504671-72505270	HCT-116	colon:	n/a	n/a
49	E2F6	chr11:72504397-72505232	H1-hESC	embryonic stem cell:	n/a	chr11:72504805-72504817 chr11:72504863-72504875 chr11:72504750-72504759 chr11:72504797-72504806 chr11:72505115-72505129
50	FOXA1	chr11:72504496-72505324	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:72502078..72507217-chr11:72523813..72527208,9	K562	blood:
2	chr11:72504689..72505257-chr12:112856305..112856856,2	Hela-S3	cervix:
3	chr11:72504451..72505136-chr11:72525016..72525872,2	MCF-7	breast:
4	chr11:72432212..72438079-chr11:72503579..72507160,8	MCF-7	breast:
5	chr11:72487526..72509577-chr11:72522325..72536312,93	MCF-7	breast:
6	chr11:72503176..72507418-chr11:72523751..72527635,5	MCF-7	breast:
7	chr11:72433323..72435429-chr11:72502768..72506514,3	K562	blood:
8	chr11:72462706..72465111-chr11:72501934..72505822,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARAP1-1	chr11:72504669-72505213	NONHSAT022799

Variant related genes	Relation type
ARAP1	TF binding region
STARD10	TF binding region
ENSG00000179295	Chromatin interaction
ENSG00000089009	Chromatin interaction
ENSG00000168010	Chromatin interaction
ENSG00000186635	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1000620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10431171	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10431172	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10431174	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10751213	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10751215	0.96[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10751216	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10898877	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898879	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898880	0.95[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10898881	0.80[JPT][hapmap]
rs11235592	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235596	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864653	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975109	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35343925	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35668754	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35752694	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4459331	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4459332	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs485099	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944797	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944800	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944802	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944805	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs519790	0.91[YRI][hapmap]
rs6592486	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592489	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6592490	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7110719	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7952617	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][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	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
3	nsv825992	chr11:72476174-72524295	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs677231	STARD10	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72503800-72506200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr11:72504000-72505000	Flanking Active TSS	Fetal Brain Male	brain
3	chr11:72504000-72505800	Enhancers	Small Intestine	intestine
4	chr11:72504200-72505400	Active TSS	Colonic Mucosa	Colon
5	chr11:72504200-72505600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr11:72504200-72505600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr11:72504200-72505800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr11:72504200-72506000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr11:72504400-72505200	Active TSS	Fetal Muscle Trunk	muscle
10	chr11:72504400-72505400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr11:72504400-72505400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:72504400-72505400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:72504400-72505400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr11:72504400-72505400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:72504400-72505400	Active TSS	Brain Germinal Matrix	brain
16	chr11:72504400-72505400	Active TSS	Ovary	ovary
17	chr11:72504400-72505600	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr11:72504400-72505600	Active TSS	Fetal Kidney	kidney
19	chr11:72504600-72505200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr11:72504600-72505200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr11:72504600-72505200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:72504600-72505200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:72504600-72505200	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr11:72504600-72505200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:72504600-72505200	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr11:72504600-72505200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:72504600-72505200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:72504600-72505200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr11:72504600-72505200	Active TSS	Primary T cells from cord blood	blood
30	chr11:72504600-72505200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:72504600-72505200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:72504600-72505200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:72504600-72505200	Active TSS	Muscle Satellite Cultured Cells	--
34	chr11:72504600-72505200	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr11:72504600-72505200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:72504600-72505200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:72504600-72505200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:72504600-72505200	Active TSS	Adipose Nuclei	Adipose
39	chr11:72504600-72505200	Active TSS	Duodenum Mucosa	Duodenum
40	chr11:72504600-72505200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr11:72504600-72505200	Active TSS	Fetal Intestine Small	intestine
42	chr11:72504600-72505200	Active TSS	Fetal Lung	lung
43	chr11:72504600-72505200	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr11:72504600-72505200	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr11:72504600-72505200	Active TSS	Rectal Smooth Muscle	rectum
46	chr11:72504600-72505200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr11:72504600-72505200	Active TSS	Stomach Mucosa	stomach
48	chr11:72504600-72505200	Active TSS	Thymus	Thymus
49	chr11:72504600-72505200	Active TSS	Spleen	Spleen
50	chr11:72504600-72505200	Active TSS	A549	lung

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