Variant report

Variant	rs2293962
Chromosome Location	chr10:38299843-38299844
allele	G/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	SP1	chr10:38299208-38300331	A549	lung:	n/a	chr10:38300044-38300053 chr10:38299758-38299771
2	CEBPB	chr10:38299190-38300530	Hela-S3	cervix:	n/a	chr10:38299297-38299310
3	POLR2A	chr10:38299249-38300334	K562	blood:	n/a	n/a
4	YY1	chr10:38299758-38300146	HCT-116	colon:	n/a	chr10:38299936-38299947 chr10:38299771-38299782
5	CTCF	chr10:38299720-38299870	NHEK	skin:	n/a	chr10:38299771-38299784
6	TBP	chr10:38299166-38300267	K562	blood:	n/a	n/a
7	POLR2A	chr10:38299176-38300256	HUVEC	blood vessel:	n/a	n/a
8	ELF1	chr10:38299324-38300217	A549	lung:	n/a	chr10:38299761-38299773
9	MYC	chr10:38299129-38300259	K562	blood:	n/a	chr10:38299771-38299781
10	CBX3	chr10:38299064-38300203	K562	blood:	n/a	n/a
11	TCF12	chr10:38299198-38300347	ECC-1	luminal epithelium:	n/a	chr10:38299417-38299427 chr10:38299219-38299226
12	ZNF263	chr10:38299273-38300236	HEK293-T-REx	kidney:	n/a	chr10:38299797-38299806
13	MAX	chr10:38299157-38300264	HCT-116	colon:	n/a	chr10:38299771-38299781
14	CTCF	chr10:38299800-38299950	WERI-Rb-1	eye:	n/a	n/a
15	CTCF	chr10:38299760-38299910	Caco-2	colon:	n/a	chr10:38299771-38299784
16	YY1	chr10:38299689-38300185	GM12891	blood:	n/a	chr10:38299936-38299947 chr10:38299771-38299782
17	RFX5	chr10:38299305-38300170	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr10:38299720-38299870	GM12875	blood:	n/a	chr10:38299771-38299784
19	POLR2A	chr10:38299219-38300411	Gliobla	brain:	n/a	n/a
20	CTCF	chr10:38299720-38299870	HCPEpiC	choroid plexus:	n/a	chr10:38299771-38299784
21	MAX	chr10:38299354-38300229	HepG2	liver:	n/a	chr10:38299771-38299781
22	EP300	chr10:38299830-38300197	HepG2	liver:	n/a	n/a
23	MYC	chr10:38299336-38300237	MCF-7	breast:	n/a	chr10:38299771-38299781
24	TAF1	chr10:38299593-38300219	GM12891	blood:	n/a	n/a
25	TAF1	chr10:38299225-38300232	A549	lung:	n/a	n/a
26	POLR2A	chr10:38299174-38300337	GM12878	blood:	n/a	n/a
27	CTCF	chr10:38299740-38299890	HUVEC	blood vessel:	n/a	chr10:38299771-38299784
28	MYC	chr10:38299255-38300275	K562	blood:	n/a	chr10:38299771-38299781
29	CREB1	chr10:38299191-38300294	HepG2	liver:	n/a	n/a
30	CTCF	chr10:38299740-38299890	HMF	breast:	n/a	chr10:38299771-38299784
31	ELF1	chr10:38299277-38300279	GM12878	blood:	n/a	chr10:38299761-38299773
32	ELF1	chr10:38299230-38300046	HepG2	liver:	n/a	chr10:38299761-38299773
33	TAF1	chr10:38299363-38300274	H1-neurons	neurons:	n/a	n/a
34	TCF12	chr10:38299068-38300396	A549	lung:	n/a	chr10:38299417-38299427 chr10:38299219-38299226
35	POLR2A	chr10:38299230-38300221	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr10:38299143-38300394	GM12892	blood:	n/a	n/a
37	CTCFL	chr10:38299615-38299925	K562	blood:	n/a	n/a
38	CTCF	chr10:38299740-38299890	HPAF	blood vessel:	n/a	chr10:38299771-38299784
39	TAF1	chr10:38299226-38300204	K562	blood:	n/a	n/a
40	TCF12	chr10:38299773-38300200	GM12878	blood:	n/a	n/a
41	CTCF	chr10:38299700-38299850	HCT-116	colon:	n/a	chr10:38299771-38299784
42	HCFC1	chr10:38299032-38300520	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr10:38299172-38300418	MCF-7	breast:	n/a	n/a
44	TCF7L2	chr10:38299229-38300427	HCT-116	colon:	n/a	n/a
45	FOXM1	chr10:38299221-38300562	GM12878	blood:	n/a	n/a
46	MAZ	chr10:38298955-38300421	IMR90	lung:	n/a	chr10:38299771-38299781
47	TAF1	chr10:38299166-38300341	H1-hESC	embryonic stem cell:	n/a	n/a
48	YY1	chr10:38299289-38300193	K562	blood:	n/a	chr10:38299936-38299947 chr10:38299771-38299782
49	IRF4	chr10:38299687-38300082	GM12878	blood:	n/a	n/a
50	JUND	chr10:38299619-38300244	A549	lung:	n/a	chr10:38299766-38299775

No.	Distal block	Cell Line	Cell type
1	chr10:38298494..38301362-chr10:38382665..38385531,3	K562	blood:
2	chr10:38299547..38300395-chr21:34697151..34697771,2	Hela-S3	cervix:
3	chr10:38299228..38300153-chr19:5689858..5690676,2	Hela-S3	cervix:
4	chr10:38299411..38301761-chr10:38382405..38384673,2	MCF-7	breast:
5	chr10:38299349..38301423-chr10:38382665..38385531,5	K562	blood:
6	chr10:38262821..38267029-chr10:38297888..38300843,9	MCF-7	breast:
7	chr10:38298279..38301657-chr10:38381478..38384966,6	MCF-7	breast:
8	chr10:38264781..38267519-chr10:38298501..38300973,4	MCF-7	breast:
9	chr10:38299418..38299986-chr15:64673239..64673830,2	Hela-S3	cervix:
10	chr1:241682514..241683274-chr10:38299405..38300057,2	Hela-S3	cervix:
11	chr10:38299096..38299940-chr17:80415305..80415911,2	Hela-S3	cervix:
12	chr10:38264914..38266697-chr10:38299677..38301313,2	K562	blood:

Variant related genes	Relation type
ZNF33A	TF binding region
ENSG00000226447	Chromatin interaction
ENSG00000175395	Chromatin interaction
ENSG00000130255	Chromatin interaction
ENSG00000091483	Chromatin interaction
ENSG00000075407	Chromatin interaction
ENSG00000142166	Chromatin interaction
ENSG00000265458	Chromatin interaction
ENSG00000166803	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1208578	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208619	0.80[EUR][1000 genomes]
rs1208621	0.86[EUR][1000 genomes]
rs12413083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[ASN][1000 genomes]
rs12414618	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1735625	0.84[EUR][1000 genomes]
rs17608725	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs176831	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176832	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1779073	0.88[EUR][1000 genomes]
rs200907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs200909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs200913	0.80[EUR][1000 genomes]
rs200944	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2021651	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2178958	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2472153	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472159	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2472160	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs2474545	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474553	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2480521	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2489166	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2504137	0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505218	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2738221	0.88[EUR][1000 genomes]
rs2753883	0.83[EUR][1000 genomes]
rs664543	0.84[EUR][1000 genomes]
rs677565	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs766362	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7895468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9418311	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2293962	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL
rs2293962	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38298400-38301000	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:38298600-38300400	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr10:38298800-38300200	Active TSS	Primary monocytes fromperipheralblood	blood
4	chr10:38298800-38300400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:38298800-38300400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr10:38298800-38300400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:38298800-38300400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr10:38298800-38300400	Active TSS	Colon Smooth Muscle	Colon
9	chr10:38298800-38300600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr10:38298800-38300600	Active TSS	Brain Hippocampus Middle	brain
11	chr10:38298800-38300800	Active TSS	A549	lung
12	chr10:38298800-38300800	Active TSS	HepG2	liver
13	chr10:38298800-38301000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr10:38298800-38301000	Active TSS	HMEC	breast
15	chr10:38298800-38301400	Active TSS	K562	blood
16	chr10:38299000-38300000	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr10:38299000-38300000	Active TSS	Stomach Smooth Muscle	stomach
18	chr10:38299000-38300200	Active TSS	Primary B cells from peripheral blood	blood
19	chr10:38299000-38300200	Active TSS	Primary T cells fromperipheralblood	blood
20	chr10:38299000-38300200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:38299000-38300200	Active TSS	Liver	Liver
22	chr10:38299000-38300200	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr10:38299000-38300400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr10:38299000-38300400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr10:38299000-38300400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr10:38299000-38300400	Active TSS	Brain Substantia Nigra	brain
27	chr10:38299000-38300400	Active TSS	Duodenum Mucosa	Duodenum
28	chr10:38299000-38300400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr10:38299000-38300400	Active TSS	Fetal Lung	lung
30	chr10:38299000-38300400	Active TSS	Placenta	Placenta
31	chr10:38299000-38300400	Active TSS	Fetal Thymus	thymus
32	chr10:38299000-38300400	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr10:38299000-38300400	Active TSS	Thymus	Thymus
34	chr10:38299000-38300400	Active TSS	NH-A	brain
35	chr10:38299000-38300400	Active TSS	NHLF	lung
36	chr10:38299000-38300600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr10:38299000-38300600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr10:38299000-38300600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:38299000-38300600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr10:38299000-38300600	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr10:38299000-38300600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr10:38299000-38300600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:38299000-38300600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:38299000-38300600	Active TSS	Brain Angular Gyrus	brain
45	chr10:38299000-38300600	Active TSS	Brain Anterior Caudate	brain
46	chr10:38299000-38300600	Active TSS	Brain Cingulate Gyrus	brain
47	chr10:38299000-38300600	Active TSS	Fetal Brain Male	brain
48	chr10:38299000-38300600	Active TSS	Fetal Brain Female	brain
49	chr10:38299000-38300600	Active TSS	Fetal Stomach	stomach
50	chr10:38299000-38300600	Active TSS	Placenta Amnion	Placenta Amnion

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