Variant report

Variant	rs59572505
Chromosome Location	chr7:150014986-150014987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr7:150014887-150015398	K562	blood:	n/a	n/a
2	GATA2	chr7:150014760-150015556	K562	blood:	n/a	n/a
3	MAFF	chr7:150014798-150015439	K562	blood:	n/a	n/a
4	STAT5A	chr7:150014788-150015553	K562	blood:	n/a	n/a
5	PML	chr7:150014658-150015534	K562	blood:	n/a	n/a
6	POLR2A	chr7:150014543-150015128	Hela-S3	cervix:	n/a	n/a
7	JUND	chr7:150014798-150015523	K562	blood:	n/a	n/a
8	NR2F2	chr7:150014741-150015487	K562	blood:	n/a	n/a
9	MYC	chr7:150014966-150015487	K562	blood:	n/a	n/a
10	FOS	chr7:150014884-150015440	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr7:150014833-150015473	K562	blood:	n/a	n/a
12	CEBPD	chr7:150014733-150015597	K562	blood:	n/a	n/a
13	KAP1	chr7:150014794-150015465	K562	blood:	n/a	n/a
14	TBP	chr7:150014859-150015459	K562	blood:	n/a	n/a
15	TBL1XR1	chr7:150014656-150015559	K562	blood:	n/a	n/a
16	TRIM28	chr7:150014880-150015542	K562	blood:	n/a	n/a
17	IRF1	chr7:150014752-150015455	K562	blood:	n/a	n/a
18	EP300	chr7:150014745-150015570	K562	blood:	n/a	n/a
19	NR2F2	chr7:150014672-150015591	K562	blood:	n/a	n/a
20	STAT5A	chr7:150014742-150015604	K562	blood:	n/a	n/a
21	RCOR1	chr7:150014861-150015458	K562	blood:	n/a	n/a
22	TRIM28	chr7:150014772-150015617	K562	blood:	n/a	n/a
23	CBX3	chr7:150014685-150015915	K562	blood:	n/a	n/a
24	POLR2A	chr7:150014766-150015478	K562	blood:	n/a	n/a
25	REST	chr7:150014887-150015445	K562	blood:	n/a	n/a
26	EP300	chr7:150014548-150015552	K562	blood:	n/a	n/a
27	RCOR1	chr7:150014834-150015556	K562	blood:	n/a	n/a
28	CCNT2	chr7:150014932-150015514	K562	blood:	n/a	n/a
29	BHLHE40	chr7:150014952-150015517	K562	blood:	n/a	n/a
30	ATF1	chr7:150014935-150015449	K562	blood:	n/a	n/a
31	JUN	chr7:150014681-150015481	K562	blood:	n/a	n/a
32	POLR2A	chr7:150014873-150015047	HepG2	liver:	n/a	n/a
33	TEAD4	chr7:150014700-150015528	K562	blood:	n/a	n/a
34	MYC	chr7:150014818-150015517	K562	blood:	n/a	n/a
35	TEAD4	chr7:150014543-150015633	K562	blood:	n/a	n/a
36	JUN	chr7:150014270-150015739	K562	blood:	n/a	n/a
37	CUX1	chr7:150014635-150015504	K562	blood:	n/a	n/a
38	MAFK	chr7:150014770-150015437	K562	blood:	n/a	n/a
39	JUN	chr7:150014943-150015462	K562	blood:	n/a	n/a
40	JUND	chr7:150014955-150015367	H1-hESC	embryonic stem cell:	n/a	n/a
41	UBTF	chr7:150014883-150015435	K562	blood:	n/a	n/a
42	UBTF	chr7:150014888-150015251	K562	blood:	n/a	n/a
43	TAL1	chr7:150014735-150015472	K562	blood:	n/a	n/a
44	ARID3A	chr7:150014510-150015466	K562	blood:	n/a	n/a
45	ZMIZ1	chr7:150014805-150015525	K562	blood:	n/a	n/a
46	RFX5	chr7:150014759-150015151	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:150014201..150017150-chr7:150057916..150059881,2	K562	blood:
2	chr7:150014370..150017313-chr7:150124547..150126790,2	K562	blood:
3	chr7:150013799..150016585-chr7:150070801..150072302,2	K562	blood:
4	chr7:150013473..150016267-chr7:150116910..150118946,2	K562	blood:
5	chr7:150010873..150012511-chr7:150013299..150015107,2	MCF-7	breast:
6	chr7:150013529..150015903-chr7:150058495..150060887,2	K562	blood:
7	chr7:150011213..150016878-chr7:150064606..150067835,7	K562	blood:
8	chr7:150009392..150012620-chr7:150013659..150016251,3	MCF-7	breast:

No data

Variant related genes	Relation type
LRRC61	TF binding region
ENSG00000196456	Chromatin interaction
ENSG00000214022	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10952249	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10952250	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11764936	0.85[EUR][1000 genomes]
rs11765644	0.85[EUR][1000 genomes]
rs11765692	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11766288	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11767726	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11769348	0.85[EUR][1000 genomes]
rs11773351	0.83[EUR][1000 genomes]
rs11974980	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11975886	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11983355	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1464752	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1464753	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17837498	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1916932	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1962004	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1983440	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2108851	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2108852	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2108853	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2108854	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159234	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2159235	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159236	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373751	0.85[EUR][1000 genomes]
rs3088207	0.83[EUR][1000 genomes]
rs3735169	0.83[EUR][1000 genomes]
rs3735170	0.83[EUR][1000 genomes]
rs3735171	0.84[EUR][1000 genomes]
rs3735172	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3735173	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3735174	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3735175	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800780	0.85[EUR][1000 genomes]
rs3800781	0.85[EUR][1000 genomes]
rs4395803	0.85[EUR][1000 genomes]
rs4554381	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55715989	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55881542	0.85[EUR][1000 genomes]
rs56019796	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56190213	0.85[EUR][1000 genomes]
rs56402329	0.81[EUR][1000 genomes]
rs56923535	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56998970	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57888387	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60268791	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60283368	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60467296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73170169	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73170174	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170185	0.85[EUR][1000 genomes]
rs7781827	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7788316	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806429	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv508490	chr7:150006068-150051241	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv889453	chr7:150009838-150104410	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv889454	chr7:150009838-150115183	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv889455	chr7:150013393-150104410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv889456	chr7:150013393-150115183	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs59572505	LRRC61	cis	Nerve Tibial	GTEx
rs59572505	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs59572505	LRRC61	cis	Esophagus Mucosa	GTEx
rs59572505	LRRC61	cis	Muscle Skeletal	GTEx
rs59572505	LRRC61	cis	Artery Tibial	GTEx
rs59572505	REPIN1	cis	Muscle Skeletal	GTEx
rs59572505	LRRC61	cis	Whole Blood	GTEx
rs59572505	LRRC61	cis	lung	GTEx
rs59572505	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs59572505	LRRC61	cis	Adipose Subcutaneous	GTEx
rs59572505	ZBED6CL	cis	lung	GTEx
rs59572505	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs59572505	LRRC61	cis	Heart Left Ventricle	GTEx
rs59572505	LRRC61	cis	Thyroid	GTEx
rs59572505	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs59572505	ZBED6CL	cis	Esophagus Mucosa	GTEx
rs59572505	RARRES2	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149984200-150019400	Weak transcription	Colonic Mucosa	Colon
2	chr7:149992400-150018000	Weak transcription	Fetal Intestine Small	intestine
3	chr7:150003800-150016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:150004000-150019000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:150007000-150015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:150007600-150018000	Weak transcription	Fetal Intestine Large	intestine
7	chr7:150009400-150017000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:150009400-150020000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:150009600-150016000	Weak transcription	GM12878-XiMat	blood
10	chr7:150009800-150017000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:150010200-150017000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr7:150010400-150018200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr7:150011000-150019000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:150011000-150019600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:150011200-150016400	Weak transcription	Esophagus	oesophagus
16	chr7:150011200-150019200	Weak transcription	Spleen	Spleen
17	chr7:150011400-150015000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:150011400-150016800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:150011400-150017200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:150011400-150017600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr7:150011400-150019000	Weak transcription	Gastric	stomach
22	chr7:150011600-150019000	Weak transcription	Stomach Mucosa	stomach
23	chr7:150012800-150019000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:150013200-150019200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:150013400-150016800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:150014000-150017800	Weak transcription	HepG2	liver
27	chr7:150014000-150018000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:150014000-150019000	Weak transcription	Primary T cells from cord blood	blood
29	chr7:150014000-150019200	Weak transcription	Primary B cells from cord blood	blood
30	chr7:150014200-150016800	Weak transcription	Hela-S3	cervix
31	chr7:150014200-150018200	Weak transcription	NHLF	lung
32	chr7:150014400-150016200	Weak transcription	Placenta	Placenta
33	chr7:150014400-150016400	Weak transcription	Liver	Liver
34	chr7:150014400-150016400	Weak transcription	Pancreas	Pancrea
35	chr7:150014400-150018200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr7:150014600-150015200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr7:150014600-150015600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr7:150014600-150015800	Flanking Active TSS	K562	blood
39	chr7:150014600-150016200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr7:150014800-150015000	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr7:150014800-150015200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr7:150014800-150015200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:150014800-150015200	Enhancers	NH-A	brain
44	chr7:150014800-150015400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr7:150014800-150015400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:150014800-150015600	Enhancers	HUVEC	blood vessel

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