Variant report

Variant	rs574997
Chromosome Location	chr5:179309513-179309514
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr5:179309398-179309736	U2OS	brain:	n/a	n/a
2	SETDB1	chr5:179309305-179310567	K562	blood:	n/a	n/a
3	KAP1	chr5:179309334-179309692	K562	blood:	n/a	n/a
4	CBX3	chr5:179309332-179309677	K562	blood:	n/a	n/a
5	CBX3	chr5:179309270-179309637	K562	blood:	n/a	n/a
6	POLR2A	chr5:179309470-179310038	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179308524..179311732-chr5:179312804..179315984,3	K562	blood:
2	chr5:179305874..179308839-chr5:179309473..179313731,6	MCF-7	breast:
3	chr5:179307319..179310872-chr5:179333429..179336113,3	MCF-7	breast:
4	chr5:179299709..179302436-chr5:179308085..179309910,2	MCF-7	breast:

No data

Variant related genes	Relation type
TBC1D9B	TF binding region
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs152233	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152236	0.84[ASN][1000 genomes]
rs152237	0.84[ASN][1000 genomes]
rs152238	0.84[ASN][1000 genomes]
rs155791	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs155795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs155796	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs155797	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs156101	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs156104	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1684973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182086	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2431123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2431124	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs248218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248220	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs248222	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248232	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26074	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26075	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs26077	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs26078	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27471	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27474	0.82[ASN][1000 genomes]
rs28325	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30381	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30382	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30385	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30386	0.87[CHD][hapmap];0.82[MEX][hapmap]
rs32437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32461	0.93[ASN][1000 genomes]
rs32469	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32470	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32471	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs32472	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3734003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs43155	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs532795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578659	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs860706	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs88183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9957	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
7	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
9	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
10	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
11	nsv883286	chr5:179290845-179313656	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs574997	BTNL9	cis	cerebellum	SCAN
rs574997	C5orf45	cis	cerebellum	SCAN
rs574997	HIGD2A	cis	cerebellum	SCAN
rs574997	TBC1D9B	cis	Muscle Skeletal	GTEx
rs574997	SLC34A1	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179286200-179310600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179286600-179310600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr5:179286600-179310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:179286600-179311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:179287200-179333600	Weak transcription	Right Atrium	heart
6	chr5:179287800-179310000	Weak transcription	Fetal Brain Male	brain
7	chr5:179288400-179310600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:179289600-179328000	Strong transcription	Adipose Nuclei	Adipose
9	chr5:179290400-179309600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:179295200-179334000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:179299800-179309600	Weak transcription	K562	blood
12	chr5:179300400-179310200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:179302200-179310600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:179302400-179310800	Weak transcription	Psoas Muscle	Psoas
15	chr5:179302600-179309600	Weak transcription	NH-A	brain
16	chr5:179303800-179309800	Weak transcription	Primary B cells from cord blood	blood
17	chr5:179303800-179309800	Weak transcription	Fetal Kidney	kidney
18	chr5:179304600-179309800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:179304600-179310600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr5:179305200-179309800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:179305200-179310600	Weak transcription	HSMMtube	muscle
22	chr5:179305600-179309600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:179305800-179310600	Weak transcription	Hela-S3	cervix
24	chr5:179306000-179309800	Weak transcription	HSMM	muscle
25	chr5:179306600-179309600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:179306800-179309800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:179306800-179310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:179306800-179310800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:179306800-179311600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:179307000-179309800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:179307000-179309800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:179307000-179310600	Weak transcription	Brain Substantia Nigra	brain
33	chr5:179307000-179310600	Weak transcription	Left Ventricle	heart
34	chr5:179307400-179309600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:179307400-179310400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:179307600-179310800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:179307600-179310800	Weak transcription	Aorta	Aorta
38	chr5:179307800-179310600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:179308000-179310600	Weak transcription	Colonic Mucosa	Colon
40	chr5:179308200-179309600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr5:179308200-179309600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:179308200-179309800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:179308200-179310200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:179308200-179310600	Weak transcription	NHLF	lung
45	chr5:179308400-179309600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:179308400-179309600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:179308400-179309600	Weak transcription	Ovary	ovary
48	chr5:179308400-179309800	Weak transcription	Gastric	stomach
49	chr5:179308400-179309800	Weak transcription	Pancreas	Pancrea
50	chr5:179308400-179310000	Weak transcription	Colon Smooth Muscle	Colon

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