Variant report

Variant	rs1006169
Chromosome Location	chr7:97938443-97938444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97937242..97938860-chr7:97939013..97940800,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272782	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10953254	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11768214	0.83[ASN][1000 genomes]
rs11768599	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11769950	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772432	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12533982	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12536125	0.81[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs12539761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1541409	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1874344	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1985593	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2107718	0.81[TSI][hapmap]
rs2240348	0.81[ASW][hapmap];1.00[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];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270597	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2270603	0.82[MEX][hapmap]
rs3735258	0.90[ASW][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs3801258	0.81[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816943	0.82[MEX][hapmap]
rs3944111	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4236537	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4729432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55648546	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55946416	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56997921	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59120980	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62478160	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62478201	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62478228	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62478235	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62479844	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62479858	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs903592	0.91[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs9640655	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9641236	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9641237	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9649213	0.82[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv1016826	chr7:97926133-97963717	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised 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
rs1006169	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs1006169	FIS1	cis	cerebellum	SCAN
rs1006169	FIS1	cis	parietal	SCAN
rs1006169	PILRB	cis	parietal	SCAN
rs1006169	DKFZP434B0335	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97914200-97958400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:97919000-97941200	Weak transcription	Psoas Muscle	Psoas
3	chr7:97919200-97957600	Weak transcription	Right Atrium	heart
4	chr7:97922200-97946800	Weak transcription	Small Intestine	intestine
5	chr7:97923000-97942600	Weak transcription	Primary B cells from cord blood	blood
6	chr7:97923400-97952000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:97924600-97952200	Weak transcription	Fetal Kidney	kidney
8	chr7:97924600-97952800	Weak transcription	NH-A	brain
9	chr7:97924800-97942600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:97925000-97939000	Weak transcription	Brain Angular Gyrus	brain
11	chr7:97925200-97941600	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:97926600-97942600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:97927000-97942600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:97927200-97939200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:97927600-97940400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:97927600-97948200	Weak transcription	Brain Germinal Matrix	brain
17	chr7:97928200-97939200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr7:97928800-97947400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr7:97929400-97939600	Strong transcription	Lung	lung
20	chr7:97929400-97942000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:97929400-97945200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr7:97929400-97945800	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr7:97929400-97947400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr7:97930600-97939200	Weak transcription	Brain Substantia Nigra	brain
25	chr7:97930800-97941600	Weak transcription	K562	blood
26	chr7:97931400-97942000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:97932000-97941600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:97933000-97948400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr7:97933600-97952000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:97933800-97947000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr7:97934800-97940800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:97934800-97941800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:97934800-97942000	Strong transcription	Liver	Liver
34	chr7:97934800-97942600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:97934800-97942800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:97934800-97947400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr7:97935200-97940400	Strong transcription	Colonic Mucosa	Colon
38	chr7:97935200-97943000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:97935200-97946000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr7:97935400-97939200	Strong transcription	Adipose Nuclei	Adipose
41	chr7:97935400-97939200	Strong transcription	Rectal Smooth Muscle	rectum
42	chr7:97935400-97940000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:97935600-97938800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:97935600-97939200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:97935600-97939200	Strong transcription	Osteobl	bone
46	chr7:97935600-97941600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr7:97935600-97942600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:97935800-97939200	Strong transcription	Placenta	Placenta
49	chr7:97935800-97939600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr7:97935800-97941800	Strong transcription	Fetal Intestine Large	intestine

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