Variant report

Variant	rs10786368
Chromosome Location	chr10:99496361-99496362
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	MBD4	chr10:99496234-99496952	HepG2	liver:	n/a	n/a
2	CBX3	chr10:99496326-99497095	K562	blood:	n/a	n/a
3	POLR2A	chr10:99496137-99497519	Raji	blood:	n/a	n/a
4	BCL3	chr10:99496279-99497847	A549	lung:	n/a	chr10:99497145-99497158
5	MAX	chr10:99496288-99497454	GM12878	blood:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
6	USF2	chr10:99496011-99497139	GM12878	blood:	n/a	n/a
7	STAT5A	chr10:99496253-99497764	GM12878	blood:	n/a	n/a
8	SP4	chr10:99496332-99497138	H1-hESC	embryonic stem cell:	n/a	chr10:99496827-99496843
9	POLR2A	chr10:99496359-99497476	GM12878	blood:	n/a	n/a
10	EGR1	chr10:99496336-99497778	HCT-116	colon:	n/a	chr10:99497439-99497454 chr10:99496522-99496546 chr10:99496824-99496839 chr10:99497440-99497453 chr10:99497440-99497453 chr10:99496789-99496798
11	POLR2A	chr10:99496313-99497771	GM12878	blood:	n/a	n/a
12	MYC	chr10:99496353-99497545	NB4	blood:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
13	RCOR1	chr10:99496308-99497072	Hela-S3	cervix:	n/a	n/a
14	ELF1	chr10:99496330-99497788	MCF-7	breast:	n/a	n/a
15	CHD2	chr10:99496223-99496827	K562	blood:	n/a	n/a
16	CHD2	chr10:99496360-99497560	GM12878	blood:	n/a	n/a
17	MAX	chr10:99496287-99497409	H1-hESC	embryonic stem cell:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
18	MAX	chr10:99496200-99497323	A549	lung:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
19	POLR2A	chr10:99496349-99497984	GM12891	blood:	n/a	n/a
20	ELF1	chr10:99496353-99497261	A549	lung:	n/a	n/a
21	E2F6	chr10:99496139-99497238	A549	lung:	n/a	chr10:99496778-99496785 chr10:99496855-99496864 chr10:99496778-99496785 chr10:99496857-99496866 chr10:99496789-99496798 chr10:99496778-99496785 chr10:99496774-99496786
22	POLR2A	chr10:99496125-99497650	GM15510	blood:	n/a	n/a
23	E2F6	chr10:99495990-99497191	H1-hESC	embryonic stem cell:	n/a	chr10:99496778-99496785 chr10:99496855-99496864 chr10:99496778-99496785 chr10:99496857-99496866 chr10:99496789-99496798 chr10:99496778-99496785 chr10:99496774-99496786
24	E2F6	chr10:99496231-99497305	H1-hESC	embryonic stem cell:	n/a	chr10:99496778-99496785 chr10:99496855-99496864 chr10:99496778-99496785 chr10:99496857-99496866 chr10:99496789-99496798 chr10:99496778-99496785 chr10:99496774-99496786
25	ATF3	chr10:99496360-99497040	A549	lung:	n/a	chr10:99496857-99496864 chr10:99496855-99496868 chr10:99496857-99496865 chr10:99496856-99496864 chr10:99496845-99496865 chr10:99496851-99496865 chr10:99496854-99496864 chr10:99496853-99496864 chr10:99496854-99496867 chr10:99496856-99496876 chr10:99496853-99496868 chr10:99496857-99496867 chr10:99496854-99496865
26	POLR2A	chr10:99496061-99497907	GM18505	blood:	n/a	n/a
27	MAX	chr10:99496224-99497490	MCF-7	breast:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
28	REST	chr10:99496242-99497909	H1-neurons	neurons:	n/a	chr10:99496827-99496840
29	KAP1	chr10:99496323-99497844	HEK293	kidney:	n/a	n/a
30	MAX	chr10:99496094-99497652	HepG2	liver:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
31	POLR2A	chr10:99496061-99498169	GM12891	blood:	n/a	n/a
32	POLR2A	chr10:99496231-99497309	PFSK-1	brain:	n/a	n/a
33	SETDB1	chr10:99496255-99496916	U2OS	brain:	n/a	chr10:99496789-99496798
34	POLR2A	chr10:99496268-99498505	GM12878	blood:	n/a	n/a
35	E2F6	chr10:99496055-99497382	K562	blood:	n/a	chr10:99496778-99496785 chr10:99496855-99496864 chr10:99496778-99496785 chr10:99497296-99497306 chr10:99496857-99496866 chr10:99496789-99496798 chr10:99496778-99496785 chr10:99496774-99496786
36	POLR2A	chr10:99496299-99497527	ECC-1	luminal epithelium:	n/a	n/a
37	MAX	chr10:99496223-99497490	MCF-7	breast:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
38	MAX	chr10:99496136-99497613	H1-hESC	embryonic stem cell:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
39	POLR2A	chr10:99496229-99497881	GM12891	blood:	n/a	n/a
40	PAX5	chr10:99496201-99497673	GM12878	blood:	n/a	n/a
41	NFIC	chr10:99496343-99497246	ECC-1	luminal epithelium:	n/a	n/a
42	MAX	chr10:99496122-99497471	A549	lung:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
43	REST	chr10:99496155-99497099	A549	lung:	n/a	chr10:99496827-99496840
44	ATF2	chr10:99496226-99497092	H1-hESC	embryonic stem cell:	n/a	chr10:99496853-99496867
45	SMARCC1	chr10:99496361-99497882	Hela-S3	cervix:	n/a	n/a
46	MAX	chr10:99496033-99497619	A549	lung:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710
47	ELF1	chr10:99496275-99497383	HCT-116	colon:	n/a	n/a
48	POLR2A	chr10:99496080-99497138	HCT-116	colon:	n/a	n/a
49	TBP	chr10:99496189-99497094	K562	blood:	n/a	n/a
50	MAX	chr10:99496330-99497345	SK-N-SH	brain:	n/a	chr10:99496699-99496710 chr10:99496698-99496708 chr10:99496698-99496711 chr10:99496698-99496711 chr10:99496700-99496709 chr10:99496696-99496711 chr10:99496699-99496710

No.	Distal block	Cell Line	Cell type
1	chr10:99446145..99449629-chr10:99495749..99499452,3	K562	blood:
2	chr10:99460267..99463088-chr10:99494596..99496762,2	K562	blood:
3	chr10:99495273..99496977-chr10:99508285..99510585,2	MCF-7	breast:
4	chr10:99496214..99498358-chr10:99509556..99512391,2	K562	blood:
5	chr10:99445750..99450066-chr10:99494053..99497713,5	MCF-7	breast:
6	chr10:99472472..99476089-chr10:99494153..99498366,9	MCF-7	breast:
7	chr10:99471547..99474270-chr10:99495747..99497533,2	K562	blood:
8	chr10:99472128..99477527-chr10:99495091..99498402,11	MCF-7	breast:
9	chr10:99446264..99449966-chr10:99495266..99498485,3	MCF-7	breast:
10	chr10:99256761..99259494-chr10:99495841..99497583,3	K562	blood:

Variant related genes	Relation type
ZFYVE27	TF binding region
ENSG00000119986	Chromatin interaction
ENSG00000155256	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000155254	Chromatin interaction
ENSG00000165886	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10748707	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10786369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1253023	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3818876	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829137	0.84[MEX][hapmap]
rs4593946	0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4917783	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4917784	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4917785	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4919135	0.91[YRI][hapmap]
rs7076831	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7900119	0.91[YRI][hapmap]
rs7915100	0.91[YRI][hapmap]
rs946779	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946780	0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.90[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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10786368	MARVELD1	cis	Thyroid	GTEx
rs10786368	PI4K2A	cis	parietal	SCAN
rs10786368	MARVELD1	cis	lung	GTEx
rs10786368	SEMA4G	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99478800-99496400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:99486800-99496400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:99486800-99496400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr10:99486800-99496400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr10:99486800-99496400	Weak transcription	Pancreas	Pancrea
6	chr10:99486800-99496600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:99487000-99496400	Weak transcription	Brain Anterior Caudate	brain
8	chr10:99487000-99496400	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:99487000-99496400	Weak transcription	A549	lung
10	chr10:99487200-99496400	Weak transcription	NHEK	skin
11	chr10:99487200-99496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:99491600-99496400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr10:99491600-99496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:99491600-99496400	Weak transcription	Brain Substantia Nigra	brain
15	chr10:99491600-99496400	Weak transcription	NHDF-Ad	bronchial
16	chr10:99491600-99496400	Weak transcription	NHLF	lung
17	chr10:99491800-99496400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:99492000-99496400	Weak transcription	HSMM	muscle
19	chr10:99492000-99496400	Weak transcription	Osteobl	bone
20	chr10:99492200-99496400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr10:99495400-99496400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr10:99495400-99496800	Weak transcription	Aorta	Aorta
23	chr10:99495400-99497000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr10:99496000-99496400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr10:99496000-99496400	Enhancers	Primary B cells from peripheral blood	blood
26	chr10:99496000-99496400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr10:99496000-99496400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr10:99496000-99496400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr10:99496000-99496400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr10:99496000-99496600	Enhancers	HMEC	breast
31	chr10:99496000-99496600	Enhancers	K562	blood
32	chr10:99496200-99496400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr10:99496200-99496400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr10:99496200-99496400	Enhancers	Primary T cells from cord blood	blood
35	chr10:99496200-99496400	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr10:99496200-99496400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr10:99496200-99496400	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr10:99496200-99496400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr10:99496200-99496400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:99496200-99496400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr10:99496200-99496400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr10:99496200-99496400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr10:99496200-99496400	Enhancers	Adipose Nuclei	Adipose
44	chr10:99496200-99496400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr10:99496200-99496400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:99496200-99496400	Enhancers	Fetal Brain Male	brain
47	chr10:99496200-99496400	Enhancers	Fetal Brain Female	brain
48	chr10:99496200-99496400	Enhancers	Lung	lung
49	chr10:99496200-99496400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr10:99496200-99496400	Active TSS	Stomach Smooth Muscle	stomach

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