Variant report

Variant	rs624359
Chromosome Location	chr10:38299132-38299133
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	MYC	chr10:38299129-38300259	K562	blood:	n/a	chr10:38299771-38299781
2	CBX3	chr10:38299064-38300203	K562	blood:	n/a	n/a
3	TCF12	chr10:38299068-38300396	A549	lung:	n/a	chr10:38299417-38299427 chr10:38299219-38299226
4	HCFC1	chr10:38299032-38300520	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr10:38298955-38300421	IMR90	lung:	n/a	chr10:38299771-38299781
6	ELF1	chr10:38299070-38300256	HCT-116	colon:	n/a	chr10:38299761-38299773
7	RUNX3	chr10:38299049-38300583	GM12878	blood:	n/a	n/a
8	EGR1	chr10:38299074-38300491	HCT-116	colon:	n/a	chr10:38300039-38300052 chr10:38300035-38300057 chr10:38299368-38299390 chr10:38299374-38299384 chr10:38299373-38299386 chr10:38300040-38300051 chr10:38300041-38300051 chr10:38299504-38299528 chr10:38299958-38299967 chr10:38300041-38300051 chr10:38300039-38300053 chr10:38300039-38300052 chr10:38299935-38299945 chr10:38300039-38300052 chr10:38300039-38300052 chr10:38299373-38299386 chr10:38300040-38300051 chr10:38299699-38299713 chr10:38300042-38300051
9	MAX	chr10:38299063-38300422	A549	lung:	n/a	chr10:38299771-38299781
10	HEY1	chr10:38299112-38300332	HepG2	liver:	n/a	chr10:38299829-38299844
11	REST	chr10:38299108-38300253	A549	lung:	n/a	chr10:38299497-38299510
12	JUND	chr10:38299069-38300254	K562	blood:	n/a	chr10:38299766-38299775
13	POLR2A	chr10:38299077-38300714	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr10:38299109-38300365	GM12878	blood:	n/a	n/a
15	MYBL2	chr10:38299041-38300190	HepG2	liver:	n/a	n/a
16	STAT5A	chr10:38299077-38299693	GM12878	blood:	n/a	n/a
17	RELA	chr10:38299104-38300462	GM12891	blood:	n/a	n/a
18	SRF	chr10:38299132-38300175	MCF-7	breast:	n/a	n/a
19	CREB1	chr10:38299117-38300319	GM12878	blood:	n/a	n/a
20	POLR2A	chr10:38299070-38300441	GM12892	blood:	n/a	n/a
21	POLR2A	chr10:38299104-38300401	K562	blood:	n/a	n/a
22	POLR2A	chr10:38299082-38300260	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr10:38299086-38300628	GM12891	blood:	n/a	n/a
24	JUN	chr10:38298878-38300139	K562	blood:	n/a	chr10:38299766-38299775
25	SPI1	chr10:38299029-38299421	HL-60	blood:	n/a	chr10:38299223-38299236
26	ZMIZ1	chr10:38299108-38300241	K562	blood:	n/a	n/a
27	POLR2A	chr10:38299038-38300459	U87	brain:	n/a	n/a
28	REST	chr10:38299050-38300489	H1-neurons	neurons:	n/a	chr10:38299497-38299510
29	POLR2A	chr10:38299132-38300232	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr10:38299035-38300551	Raji	blood:	n/a	n/a
31	POLR2A	chr10:38299083-38300633	K562	blood:	n/a	n/a
32	TBP	chr10:38299088-38299666	GM12878	blood:	n/a	n/a
33	SPI1	chr10:38299060-38299327	GM12891	blood:	n/a	chr10:38299223-38299236
34	MXI1	chr10:38299045-38300495	IMR90	lung:	n/a	n/a
35	POLR2A	chr10:38299097-38300417	GM12878	blood:	n/a	n/a
36	SIN3AK20	chr10:38299033-38300466	MCF-7	breast:	n/a	n/a
37	POLR2A	chr10:38299105-38300234	HUVEC	blood vessel:	n/a	n/a
38	REST	chr10:38298992-38300298	HL-60	blood:	n/a	chr10:38299497-38299510
39	NFIC	chr10:38299057-38299715	GM12878	blood:	n/a	chr10:38299553-38299581
40	RCOR1	chr10:38299058-38300242	K562	blood:	n/a	n/a
41	POLR2A	chr10:38299087-38300332	K562	blood:	n/a	n/a
42	POLR2A	chr10:38299088-38300422	HL-60	blood:	n/a	n/a
43	POLR2A	chr10:38299102-38300295	GM12878	blood:	n/a	n/a
44	MTA3	chr10:38299101-38299613	GM12878	blood:	n/a	n/a
45	POLR2A	chr10:38298879-38300784	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr10:38299067-38300383	SK-N-MC	brain:	n/a	n/a
47	ETS1	chr10:38299109-38300180	A549	lung:	n/a	chr10:38299167-38299180 chr10:38299933-38299944 chr10:38299989-38300002
48	SPI1	chr10:38298911-38300168	HL-60	blood:	n/a	chr10:38299223-38299236
49	POLR2A	chr10:38299125-38300386	GM18505	blood:	n/a	n/a
50	ESRRA	chr10:38298733-38300951	GM12878	blood:	n/a	chr10:38299732-38299745

No.	Distal block	Cell Line	Cell type
1	chr10:38298494..38301362-chr10:38382665..38385531,3	K562	blood:
2	chr10:38262821..38267029-chr10:38297888..38300843,9	MCF-7	breast:
3	chr10:38298279..38301657-chr10:38381478..38384966,6	MCF-7	breast:
4	chr10:38264781..38267519-chr10:38298501..38300973,4	MCF-7	breast:
5	chr10:38299096..38299940-chr17:80415305..80415911,2	Hela-S3	cervix:
6	chr10:38259864..38262240-chr10:38297171..38299519,2	K562	blood:

Variant related genes	Relation type
ZNF33A	TF binding region
ENSG00000265458	Chromatin interaction
ENSG00000226447	Chromatin interaction
ENSG00000175395	Chromatin interaction
ENSG00000075407	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10764149	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10827831	0.90[JPT][hapmap]
rs11011401	0.90[JPT][hapmap]
rs11011426	0.90[JPT][hapmap]
rs1148287	0.90[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11523837	0.90[JPT][hapmap]
rs11597286	0.90[JPT][hapmap]
rs11598044	1.00[JPT][hapmap]
rs1208555	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1208556	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1208560	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1208573	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1208587	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1208591	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1208601	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1208633	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1208645	0.90[CEU][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1208658	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1212108	0.81[EUR][1000 genomes]
rs1212617	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1735621	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1735629	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1735641	0.90[EUR][1000 genomes]
rs1779068	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1779075	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2144848	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2472149	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474548	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505220	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2505233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2505255	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2738185	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2738186	0.90[JPT][hapmap]
rs2738187	0.90[JPT][hapmap]
rs2738190	0.90[JPT][hapmap]
rs2738191	0.90[JPT][hapmap]
rs2738193	0.86[JPT][hapmap]
rs2738207	0.90[JPT][hapmap]
rs2738208	1.00[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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738209	0.90[JPT][hapmap]
rs2738210	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2738219	0.90[JPT][hapmap]
rs2749563	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749575	0.90[JPT][hapmap]
rs2749577	0.90[JPT][hapmap]
rs2749586	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749587	0.90[JPT][hapmap]
rs2749588	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749589	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2753880	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2799496	0.90[JPT][hapmap]
rs2799499	0.90[JPT][hapmap]
rs2891586	1.00[JPT][hapmap]
rs3824585	0.90[JPT][hapmap]
rs594594	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs598857	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633400	0.90[JPT][hapmap]
rs637255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656126	0.91[EUR][1000 genomes]
rs658161	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs662928	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs675628	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs688608	0.94[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9417267	0.90[JPT][hapmap]
rs9417268	0.90[JPT][hapmap]
rs9417283	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9418299	0.89[JPT][hapmap]

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
rs624359	SIM2	trans	parietal	SCAN
rs624359	ZNF37A	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38296800-38299200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:38298000-38299600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr10:38298400-38299400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr10:38298400-38301000	Active TSS	Rectal Smooth Muscle	rectum
5	chr10:38298600-38299200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:38298600-38299200	Flanking Active TSS	Dnd41	blood
7	chr10:38298600-38299200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr10:38298600-38299400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr10:38298600-38300400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr10:38298800-38299200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr10:38298800-38299200	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr10:38298800-38299200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr10:38298800-38299200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr10:38298800-38299400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr10:38298800-38299600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:38298800-38300200	Active TSS	Primary monocytes fromperipheralblood	blood
17	chr10:38298800-38300400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:38298800-38300400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:38298800-38300400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:38298800-38300400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr10:38298800-38300400	Active TSS	Colon Smooth Muscle	Colon
22	chr10:38298800-38300600	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr10:38298800-38300600	Active TSS	Brain Hippocampus Middle	brain
24	chr10:38298800-38300800	Active TSS	A549	lung
25	chr10:38298800-38300800	Active TSS	HepG2	liver
26	chr10:38298800-38301000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr10:38298800-38301000	Active TSS	HMEC	breast
28	chr10:38298800-38301400	Active TSS	K562	blood
29	chr10:38299000-38299200	Active TSS	Primary hematopoietic stem cells	blood
30	chr10:38299000-38299200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr10:38299000-38299200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr10:38299000-38299200	Flanking Active TSS	Fetal Heart	heart
33	chr10:38299000-38299200	Flanking Active TSS	Osteobl	bone
34	chr10:38299000-38299400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr10:38299000-38299400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr10:38299000-38299400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr10:38299000-38299400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr10:38299000-38299400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr10:38299000-38299400	Active TSS	Right Atrium	heart
40	chr10:38299000-38299400	Flanking Active TSS	HUVEC	blood vessel
41	chr10:38299000-38299600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr10:38299000-38300000	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr10:38299000-38300000	Active TSS	Stomach Smooth Muscle	stomach
44	chr10:38299000-38300200	Active TSS	Primary B cells from peripheral blood	blood
45	chr10:38299000-38300200	Active TSS	Primary T cells fromperipheralblood	blood
46	chr10:38299000-38300200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:38299000-38300200	Active TSS	Liver	Liver
48	chr10:38299000-38300200	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr10:38299000-38300400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:38299000-38300400	Active TSS	Breast Myoepithelial Primary Cells	Breast

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