Variant report

Variant	rs730075
Chromosome Location	chr10:94050461-94050462
allele	A/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	TEAD4	chr10:94049856-94051379	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr10:94050338-94051378	GM15510	blood:	n/a	n/a
3	TAF1	chr10:94049913-94051473	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr10:94050360-94050510	GM12866	blood:	n/a	n/a
5	TBL1XR1	chr10:94050330-94050974	K562	blood:	n/a	n/a
6	EGR1	chr10:94049884-94051356	HCT-116	colon:	n/a	chr10:94051056-94051066 chr10:94050099-94050112 chr10:94050603-94050616 chr10:94050098-94050113 chr10:94050901-94050910 chr10:94050397-94050411 chr10:94050400-94050413 chr10:94051299-94051309 chr10:94050530-94050540 chr10:94050445-94050459 chr10:94050100-94050109 chr10:94050853-94050877 chr10:94050399-94050414
7	TAF1	chr10:94050030-94051398	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr10:94049971-94051421	ECC-1	luminal epithelium:	n/a	chr10:94051227-94051241 chr10:94051088-94051099 chr10:94050334-94050345 chr10:94051091-94051100 chr10:94051140-94051151 chr10:94051060-94051069 chr10:94050791-94050802 chr10:94050770-94050784
9	RAD21	chr10:94050076-94051205	SK-N-SH_RA	brain:	n/a	chr10:94050831-94050843 chr10:94050833-94050840
10	GTF2F1	chr10:94049890-94051024	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr10:94050204-94051213	K562	blood:	n/a	n/a
12	SREBP1	chr10:94049892-94051501	GM12878	blood:	n/a	n/a
13	JUND	chr10:94049943-94051264	K562	blood:	n/a	chr10:94050069-94050080
14	ZBTB7A	chr10:94049935-94051479	ECC-1	luminal epithelium:	n/a	n/a
15	PML	chr10:94049865-94051080	K562	blood:	n/a	n/a
16	PAX5	chr10:94050440-94051445	GM12892	blood:	n/a	n/a
17	EGR1	chr10:94049754-94051445	HCT-116	colon:	n/a	chr10:94051056-94051066 chr10:94050099-94050112 chr10:94050603-94050616 chr10:94050098-94050113 chr10:94050901-94050910 chr10:94050397-94050411 chr10:94050400-94050413 chr10:94051299-94051309 chr10:94050530-94050540 chr10:94050445-94050459 chr10:94050100-94050109 chr10:94050853-94050877 chr10:94050399-94050414
18	CTCF	chr10:94050380-94050530	HRE	kidney:	n/a	n/a
19	CREB1	chr10:94049883-94051564	HepG2	liver:	n/a	n/a
20	TAF1	chr10:94050266-94051319	H1-neurons	neurons:	n/a	n/a
21	CTCF	chr10:94050400-94050550	HRE	kidney:	n/a	n/a
22	MAX	chr10:94049839-94051562	ECC-1	luminal epithelium:	n/a	chr10:94050400-94050410 chr10:94051513-94051522
23	POLR2A	chr10:94050418-94051391	GM12878	blood:	n/a	n/a
24	KAP1	chr10:94049933-94051195	HEK293	kidney:	n/a	n/a
25	CREB1	chr10:94050276-94051348	GM12878	blood:	n/a	n/a
26	RAD21	chr10:94049973-94051115	Hela-S3	cervix:	n/a	chr10:94050831-94050843 chr10:94050833-94050840
27	ZNF143	chr10:94050208-94051205	K562	blood:	n/a	chr10:94050500-94050510 chr10:94050856-94050865 chr10:94050941-94050951 chr10:94050858-94050877 chr10:94050854-94050863 chr10:94050854-94050872
28	POLR2A	chr10:94050335-94051352	Gliobla	brain:	n/a	n/a
29	MAX	chr10:94049914-94050507	MCF-7	breast:	n/a	chr10:94050400-94050410
30	MTA3	chr10:94050406-94050797	GM12878	blood:	n/a	n/a
31	MAX	chr10:94049787-94051585	A549	lung:	n/a	chr10:94050400-94050410 chr10:94051513-94051522
32	CTCF	chr10:94050420-94050570	HAc	cerebellar:	n/a	n/a
33	EGR1	chr10:94050313-94051149	K562	blood:	n/a	chr10:94051056-94051066 chr10:94050603-94050616 chr10:94050901-94050910 chr10:94050397-94050411 chr10:94050400-94050413 chr10:94050530-94050540 chr10:94050445-94050459 chr10:94050853-94050877 chr10:94050399-94050414
34	GATA3	chr10:94050021-94051254	A549	lung:	n/a	n/a
35	GATA1	chr10:94050460-94051293	PBDE	blood:	n/a	n/a
36	POLR2A	chr10:94050230-94051275	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr10:94050170-94051442	GM19193	blood:	n/a	n/a
38	RCOR1	chr10:94050445-94050877	K562	blood:	n/a	n/a
39	RAD21	chr10:94050416-94051195	A549	lung:	n/a	chr10:94050831-94050843 chr10:94050833-94050840
40	ELF1	chr10:94050224-94051504	GM12878	blood:	n/a	chr10:94051091-94051100 chr10:94051060-94051069 chr10:94051234-94051246 chr10:94050569-94050581 chr10:94050799-94050808 chr10:94051056-94051068
41	BHLHE40	chr10:94050075-94051066	K562	blood:	n/a	n/a
42	MTA3	chr10:94050156-94051635	GM12878	blood:	n/a	n/a
43	TCF12	chr10:94049885-94051381	ECC-1	luminal epithelium:	n/a	n/a
44	ELF1	chr10:94050303-94051247	MCF-7	breast:	n/a	chr10:94051091-94051100 chr10:94051060-94051069 chr10:94051234-94051246 chr10:94050569-94050581 chr10:94050799-94050808 chr10:94051056-94051068
45	MAX	chr10:94049884-94051237	Hela-S3	cervix:	n/a	chr10:94050400-94050410
46	SMARCC2	chr10:94049890-94050972	Hela-S3	cervix:	n/a	chr10:94050854-94050863
47	MYC	chr10:94049952-94051530	K562	blood:	n/a	chr10:94050400-94050410 chr10:94051513-94051522
48	UBTF	chr10:94050161-94051474	K562	blood:	n/a	n/a
49	MAX	chr10:94049907-94051232	SK-N-SH	brain:	n/a	chr10:94050400-94050410
50	EGR1	chr10:94050267-94050575	GM12878	blood:	n/a	chr10:94050397-94050411 chr10:94050400-94050413 chr10:94050530-94050540 chr10:94050445-94050459 chr10:94050399-94050414

No.	Distal block	Cell Line	Cell type
1	chr10:94048555..94050723-chr10:94056799..94059082,2	K562	blood:
2	chr10:93948126..93950243-chr10:94048743..94050692,2	K562	blood:
3	chr10:93973011..93976411-chr10:94049477..94051967,3	K562	blood:
4	chr10:94050380..94051225-chrX:70585319..70586284,2	Hela-S3	cervix:
5	chr10:94049633..94050585-chr19:3557462..3558007,2	Hela-S3	cervix:
6	chr10:94050268..94050930-chr8:33341952..33342805,2	Hela-S3	cervix:

Variant related genes	Relation type
MARCH5	TF binding region
ENSG00000147133	Chromatin interaction
ENSG00000105988	Chromatin interaction
ENSG00000161091	Chromatin interaction
ENSG00000198042	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10509643	0.86[YRI][hapmap]
rs10786036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10882029	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10882034	0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10882035	0.82[ASN][1000 genomes]
rs10882036	0.82[ASN][1000 genomes]
rs10882039	0.91[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882043	0.85[ASN][1000 genomes]
rs11186848	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11186851	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs11186862	0.82[ASN][1000 genomes]
rs11186869	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11186872	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12246924	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12256461	0.91[AMR][1000 genomes]
rs12267769	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs12412346	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3740302	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4933721	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56072007	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57381242	0.82[ASN][1000 genomes]
rs66521023	0.81[ASN][1000 genomes]
rs66882667	0.90[ASN][1000 genomes]
rs7073372	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7080101	0.89[ASN][1000 genomes]
rs7085368	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7098170	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs7917088	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs932820	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9804247	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[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	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	esv3449576	chr10:94048622-94050670	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs730075	CYP26A1	cis	cerebellum	SCAN
rs730075	CYP2C19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94049600-94052000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr10:94049600-94052000	Active TSS	Hela-S3	cervix
3	chr10:94049600-94052200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr10:94049600-94052200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:94049600-94052200	Active TSS	HMEC	breast
6	chr10:94049600-94052200	Active TSS	K562	blood
7	chr10:94049600-94052400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr10:94049600-94052400	Active TSS	Right Atrium	heart
9	chr10:94049600-94052600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr10:94049600-94052600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr10:94049600-94052600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr10:94049800-94050600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr10:94049800-94050600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr10:94049800-94050600	Flanking Active TSS	Dnd41	blood
15	chr10:94049800-94050800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr10:94049800-94050800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr10:94049800-94051000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr10:94049800-94051200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:94049800-94051800	Active TSS	Brain Cingulate Gyrus	brain
20	chr10:94049800-94051800	Active TSS	Brain Hippocampus Middle	brain
21	chr10:94049800-94051800	Active TSS	Colonic Mucosa	Colon
22	chr10:94049800-94051800	Active TSS	Fetal Lung	lung
23	chr10:94049800-94051800	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr10:94049800-94051800	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr10:94049800-94052000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:94049800-94052000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:94049800-94052000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr10:94049800-94052000	Active TSS	Muscle Satellite Cultured Cells	--
29	chr10:94049800-94052000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:94049800-94052000	Active TSS	Brain Angular Gyrus	brain
31	chr10:94049800-94052000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr10:94049800-94052000	Active TSS	Fetal Brain Female	brain
33	chr10:94049800-94052000	Active TSS	Fetal Intestine Large	intestine
34	chr10:94049800-94052000	Active TSS	Fetal Kidney	kidney
35	chr10:94049800-94052000	Active TSS	Fetal Stomach	stomach
36	chr10:94049800-94052000	Active TSS	Rectal Smooth Muscle	rectum
37	chr10:94049800-94052000	Active TSS	Thymus	Thymus
38	chr10:94049800-94052000	Active TSS	A549	lung
39	chr10:94049800-94052200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr10:94049800-94052200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr10:94049800-94052200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:94049800-94052200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:94049800-94052200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr10:94049800-94052200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr10:94049800-94052200	Active TSS	Fetal Intestine Small	intestine
46	chr10:94049800-94052200	Active TSS	Pancreas	Pancrea
47	chr10:94049800-94052200	Active TSS	HSMM	muscle
48	chr10:94049800-94052200	Active TSS	NHDF-Ad	bronchial
49	chr10:94049800-94052400	Active TSS	H9 Cell Line	embryonic stem cell
50	chr10:94049800-94052400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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