Variant report

Variant	rs7806429
Chromosome Location	chr7:150013393-150013394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150011196..150014151-chr7:150016910..150019220,3	MCF-7	breast:
2	chr7:150010873..150012511-chr7:150013299..150015107,2	MCF-7	breast:
3	chr7:150011128..150013458-chr7:150017252..150018942,2	MCF-7	breast:
4	chr7:150011213..150016878-chr7:150064606..150067835,7	K562	blood:
5	chr7:150010085..150013848-chr7:150064824..150067454,3	K562	blood:

Variant related genes	Relation type
ENSG00000196456	Chromatin interaction
ENSG00000214022	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10952249	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10952250	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11764936	0.85[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11765644	0.85[EUR][1000 genomes]
rs11765692	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11766288	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11767726	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11769348	0.85[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11773351	0.83[EUR][1000 genomes]
rs11974980	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11975886	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11983355	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1464752	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1464753	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17173681	0.80[CEU][hapmap]
rs17173682	0.80[CEU][hapmap]
rs17837498	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1916932	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1962004	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs1983440	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2108851	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108852	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108853	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108854	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2159234	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2159235	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2159236	0.94[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2373751	0.85[EUR][1000 genomes]
rs3088207	0.83[EUR][1000 genomes]
rs3735167	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs3735169	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs3735170	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs3735171	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs3735172	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3735173	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3735174	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3735175	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800780	0.85[EUR][1000 genomes]
rs3800781	0.85[EUR][1000 genomes]
rs4395803	0.85[EUR][1000 genomes]
rs4554381	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55715989	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55881542	0.85[EUR][1000 genomes]
rs56019796	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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];0.92[ASN][1000 genomes]
rs56998970	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57888387	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59572505	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60268791	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60283368	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60467296	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73170169	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73170174	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73170185	0.85[EUR][1000 genomes]
rs7781827	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7788316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7800196	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889435	chr7:149585379-150013393	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs7806429	LRRC61	cis	lymphoblastoid	seeQTL
rs7806429	ZBED6CL	cis	Esophagus Mucosa	GTEx
rs7806429	RARRES2	cis	multi-tissue	Pritchard
rs7806429	MGC3036	cis	multi-tissue	Pritchard
rs7806429	LRRC61	cis	Nerve Tibial	GTEx
rs7806429	LRRC61	cis	parietal	SCAN
rs7806429	LRRC61	cis	Esophagus Mucosa	GTEx
rs7806429	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs7806429	LRRC61	cis	cerebellum	SCAN
rs7806429	LRRC61	cis	Thyroid	GTEx
rs7806429	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs7806429		cis	Lymphoblastoid	GTEx
rs7806429	RARRES2	cis	lymphoblastoid	seeQTL
rs7806429	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs7806429	LRRC61	cis	Heart Left Ventricle	GTEx
rs7806429	LRRC61	cis	Whole Blood	GTEx
rs7806429	C7orf29	cis	lymphoblastoid	seeQTL
rs7806429	LRRC61	cis	Muscle Skeletal	GTEx
rs7806429	REPIN1	cis	Muscle Skeletal	GTEx
rs7806429	LRRC61	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 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	chr7:150009800-150014800	Weak transcription	NH-A	brain
11	chr7:150009800-150017000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:150010200-150017000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:150010400-150014000	Weak transcription	NHLF	lung
14	chr7:150010400-150018200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr7:150011000-150019000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:150011000-150019600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:150011200-150016400	Weak transcription	Esophagus	oesophagus
18	chr7:150011200-150019200	Weak transcription	Spleen	Spleen
19	chr7:150011400-150014200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:150011400-150014800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:150011400-150015000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:150011400-150016800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:150011400-150017200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:150011400-150017600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:150011400-150019000	Weak transcription	Gastric	stomach
26	chr7:150011600-150014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:150011600-150014800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:150011600-150019000	Weak transcription	Stomach Mucosa	stomach
29	chr7:150012200-150013800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr7:150012400-150014000	Enhancers	HepG2	liver
31	chr7:150012400-150014400	Enhancers	Liver	Liver
32	chr7:150012400-150014400	Enhancers	Pancreas	Pancrea
33	chr7:150012600-150014200	Weak transcription	Placenta	Placenta
34	chr7:150012600-150014600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr7:150012800-150014200	Enhancers	Hela-S3	cervix
36	chr7:150012800-150019000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:150013000-150014600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:150013000-150014600	Enhancers	K562	blood
39	chr7:150013200-150019200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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