Variant report

Variant	rs3824617
Chromosome Location	chr10:46167847-46167848
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	POLR2A	chr10:46167568-46168608	GM19193	blood:	n/a	n/a
2	RCOR1	chr10:46167575-46169069	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:46167835-46168368	MCF-7	breast:	n/a	n/a
4	E2F6	chr10:46167537-46168690	H1-hESC	embryonic stem cell:	n/a	chr10:46168306-46168316 chr10:46168302-46168311 chr10:46168344-46168354 chr10:46168226-46168236
5	MXI1	chr10:46167538-46168428	GM12878	blood:	n/a	chr10:46168338-46168353
6	POLR2A	chr10:46167256-46169209	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr10:46167622-46168674	PANC-1	pancreas:	n/a	n/a
8	CEBPB	chr10:46167847-46168384	HepG2	liver:	n/a	n/a
9	CTCF	chr10:46167720-46167870	AG04449	skin:	n/a	n/a
10	CREB1	chr10:46167579-46168831	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr10:46167616-46168260	MCF-7	breast:	n/a	n/a
12	ZKSCAN1	chr10:46167689-46168509	Hela-S3	cervix:	n/a	n/a
13	YY1	chr10:46167804-46168437	SK-N-SH_RA	brain:	n/a	chr10:46168222-46168233 chr10:46168229-46168243 chr10:46168309-46168320
14	RAD21	chr10:46167845-46168358	SK-N-SH_RA	brain:	n/a	n/a
15	RAD21	chr10:46167568-46168637	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr10:46167717-46168030	GM12891	blood:	n/a	n/a
17	POLR2A	chr10:46167718-46168168	K562	blood:	n/a	n/a
18	FOXM1	chr10:46167847-46168617	GM12878	blood:	n/a	n/a
19	CTCF	chr10:46167660-46168411	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr10:46167672-46168514	Gliobla	brain:	n/a	n/a
21	SP1	chr10:46167571-46168687	A549	lung:	n/a	chr10:46168236-46168248 chr10:46168237-46168251 chr10:46168238-46168247 chr10:46168237-46168246 chr10:46168236-46168248 chr10:46168237-46168246 chr10:46168237-46168247 chr10:46168289-46168310 chr10:46168301-46168313 chr10:46168242-46168249 chr10:46168237-46168247
22	TAF1	chr10:46167629-46168741	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF1	chr10:46167808-46168589	ECC-1	luminal epithelium:	n/a	n/a
24	TAF1	chr10:46167502-46168880	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr10:46167653-46168730	A549	lung:	n/a	n/a
26	TBL1XR1	chr10:46167782-46168416	GM12878	blood:	n/a	n/a
27	POLR2A	chr10:46167565-46168883	GM18505	blood:	n/a	n/a
28	YY1	chr10:46167478-46168118	H1-hESC	embryonic stem cell:	n/a	n/a
29	MXI1	chr10:46167787-46168341	Hela-S3	cervix:	n/a	n/a
30	USF1	chr10:46167581-46167851	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr10:46167524-46168517	Hela-S3	cervix:	n/a	chr10:46168328-46168337 chr10:46168302-46168312
32	RCOR1	chr10:46167482-46168771	GM12878	blood:	n/a	n/a
33	CTCF	chr10:46167720-46167870	SAEC	small airway:	n/a	n/a
34	POLR2A	chr10:46167657-46168548	HCT-116	colon:	n/a	n/a
35	FOSL2	chr10:46167672-46168366	HepG2	liver:	n/a	n/a
36	MYC	chr10:46167699-46167911	MCF-7	breast:	n/a	n/a
37	CTCF	chr10:46167043-46169438	A549	lung:	n/a	n/a
38	RCOR1	chr10:46167469-46168638	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr10:46167645-46168625	A549	lung:	n/a	n/a
40	E2F6	chr10:46167616-46168786	A549	lung:	n/a	chr10:46168306-46168316 chr10:46168302-46168311 chr10:46168344-46168354 chr10:46168226-46168236
41	MAX	chr10:46167471-46169126	HepG2	liver:	n/a	chr10:46168328-46168337 chr10:46168302-46168312
42	POLR2A	chr10:46167686-46168657	A549	lung:	n/a	n/a
43	POLR2A	chr10:46167720-46168299	Hela-S3	cervix:	n/a	n/a
44	KAP1	chr10:46167550-46168954	HEK293	kidney:	n/a	n/a
45	POLR2A	chr10:46167596-46168548	MCF-7	breast:	n/a	n/a
46	CREB1	chr10:46167581-46169142	HepG2	liver:	n/a	n/a
47	POLR2A	chr10:46167712-46168784	MCF10A-Er-Src	breast:	n/a	n/a
48	ZNF143	chr10:46167802-46168994	H1-hESC	embryonic stem cell:	n/a	chr10:46168476-46168495 chr10:46168481-46168499 chr10:46168302-46168312 chr10:46168306-46168316
49	CEBPD	chr10:46167664-46168106	HepG2	liver:	n/a	n/a
50	USF1	chr10:46167497-46168692	ECC-1	luminal epithelium:	n/a	chr10:46168224-46168240

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:46167759..46168599-chr16:3450730..3451510,2	HCT-116	colon:

Variant related genes	Relation type
ZFAND4	TF binding region
ENSG00000140987	Chromatin interaction
ENSG00000103343	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10793618	0.81[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10793621	0.87[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1080264	0.81[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs10900227	0.90[CEU][hapmap]
rs11239558	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239559	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239564	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239565	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239567	0.92[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239570	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239577	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11239585	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11239587	0.87[ASW][hapmap];0.90[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11528544	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12217545	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12766066	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17157854	0.80[YRI][hapmap]
rs1982794	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982795	0.90[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1994426	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4949003	0.81[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs7068483	1.00[YRI][hapmap]
rs7074524	0.85[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7095806	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73289207	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7900810	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7918454	0.90[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv895113	chr10:46134013-46167847	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3392795	chr10:46147995-46170942	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1045014	chr10:46148750-46814526	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	esv2754498	chr10:46148750-47136996	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv540591	chr10:46153700-47140487	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1044906	chr10:46153700-47148281	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv540592	chr10:46153700-47148281	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv870020	chr10:46158215-47148490	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv1040524	chr10:46160537-47122043	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
14	nsv1038499	chr10:46160537-47140487	Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv540593	chr10:46160537-47140487	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv1055132	chr10:46160537-47148281	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv540594	chr10:46160537-47148281	Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3824617	AGAP4	cis	Artery Tibial	GTEx
rs3824617	ANUBL1	cis	parietal	SCAN
rs3824617	RBP3	cis	parietal	SCAN
rs3824617	ANUBL1	cis	cerebellum	SCAN
rs3824617	MARCH8	cis	cerebellum	SCAN
rs3824617	ZFAND4	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46166800-46169000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr10:46166800-46169000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr10:46167000-46168000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:46167000-46168200	Active TSS	Primary hematopoietic stem cells	blood
5	chr10:46167000-46168400	Active TSS	Colonic Mucosa	Colon
6	chr10:46167000-46168400	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr10:46167000-46168400	Active TSS	GM12878-XiMat	blood
8	chr10:46167000-46168600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr10:46167000-46168600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr10:46167000-46168600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:46167000-46168600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:46167000-46168600	Active TSS	Duodenum Mucosa	Duodenum
13	chr10:46167000-46168600	Active TSS	Psoas Muscle	Psoas
14	chr10:46167000-46168600	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr10:46167000-46168800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr10:46167000-46168800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:46167000-46168800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:46167000-46168800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr10:46167000-46168800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr10:46167000-46168800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr10:46167000-46169000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr10:46167000-46169000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:46167000-46169000	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr10:46167000-46169000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:46167000-46169000	Active TSS	Brain Hippocampus Middle	brain
26	chr10:46167000-46169000	Active TSS	Rectal Smooth Muscle	rectum
27	chr10:46167000-46169200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr10:46167000-46169200	Active TSS	Fetal Kidney	kidney
29	chr10:46167200-46168000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:46167200-46168400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:46167200-46168400	Active TSS	Primary T cells fromperipheralblood	blood
32	chr10:46167200-46168400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:46167200-46168400	Active TSS	Muscle Satellite Cultured Cells	--
34	chr10:46167200-46168400	Active TSS	Fetal Muscle Trunk	muscle
35	chr10:46167200-46168400	Active TSS	Fetal Muscle Leg	muscle
36	chr10:46167200-46168400	Active TSS	Fetal Thymus	thymus
37	chr10:46167200-46168400	Active TSS	HMEC	breast
38	chr10:46167200-46168600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr10:46167200-46168600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr10:46167200-46168600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr10:46167200-46168600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr10:46167200-46168600	Active TSS	Brain Cingulate Gyrus	brain
43	chr10:46167200-46168600	Active TSS	Colon Smooth Muscle	Colon
44	chr10:46167200-46168600	Active TSS	Fetal Heart	heart
45	chr10:46167200-46168600	Active TSS	Fetal Stomach	stomach
46	chr10:46167200-46168600	Active TSS	Stomach Mucosa	stomach
47	chr10:46167200-46168600	Active TSS	A549	lung
48	chr10:46167200-46168600	Active TSS	NHLF	lung
49	chr10:46167200-46168800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:46167200-46168800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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