Variant report

Variant	rs4720102
Chromosome Location	chr7:33147037-33147038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:33100859..33104943-chr7:33146945..33149986,6	MCF-7	breast:
2	chr7:33098744..33100464-chr7:33145455..33148099,2	K562	blood:
3	chr7:33131500..33135891-chr7:33143738..33147461,3	K562	blood:
4	chr7:32929813..32931362-chr7:33146969..33149896,3	K562	blood:
5	chr7:32766854..32769389-chr7:33145298..33147835,2	K562	blood:
6	chr7:33101504..33102499-chr7:33146693..33147349,2	K562	blood:
7	chr7:33144651..33147364-chr7:33168487..33170158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122643	Chromatin interaction
ENSG00000228015	Chromatin interaction
ENSG00000122507	Chromatin interaction
ENSG00000170852	Chromatin interaction
ENSG00000237004	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10245553	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10281469	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11760414	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11763923	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11766395	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11771864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11773214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11981778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12667849	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12672159	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17393789	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17393824	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17472290	0.87[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];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17472556	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2021562	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2021883	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2022231	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2392220	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28465403	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28633587	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28654432	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2893463	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3750121	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3847009	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4083280	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55862266	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56176900	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66617822	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66962586	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs68111021	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6947994	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6948361	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6963955	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6964595	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6976971	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6980186	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73093561	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7783079	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7800322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029220	chr7:32921484-33262190	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv830942	chr7:33048075-33246735	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv508450	chr7:33123335-33184848	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1033502	chr7:33124005-33185470	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1025361	chr7:33125663-33185470	Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv869720	chr7:33127192-33193580	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1026615	chr7:33128234-33185470	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription 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	12 gene(s)	inside rSNPs	diseases
8	nsv1020741	chr7:33130675-33185470	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1027807	chr7:33130675-33190591	Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv2761318	chr7:33130687-33185482	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv464422	chr7:33131729-33187279	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv606606	chr7:33131729-33187279	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv606607	chr7:33131729-33192502	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv464423	chr7:33131729-33192800	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv606608	chr7:33131729-33192800	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv520406	chr7:33131729-33192837	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv606609	chr7:33131729-33196354	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv1030007	chr7:33132814-33185470	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv1028637	chr7:33133742-33185470	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4720102	BBS9	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33115800-33148000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:33131200-33147400	Weak transcription	Small Intestine	intestine
3	chr7:33136400-33147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:33139000-33148200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:33142600-33147800	Weak transcription	Colonic Mucosa	Colon
6	chr7:33143000-33147400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:33143400-33147200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:33143400-33147200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:33143400-33147200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr7:33143400-33147400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:33143400-33147400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:33143400-33147800	Weak transcription	Aorta	Aorta
13	chr7:33143400-33148200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:33143400-33148200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:33143400-33148200	Weak transcription	Esophagus	oesophagus
16	chr7:33143400-33148200	Weak transcription	Gastric	stomach
17	chr7:33144400-33147400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr7:33144800-33147400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr7:33145000-33147600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:33145400-33147400	Enhancers	Colon Smooth Muscle	Colon
21	chr7:33145400-33147400	Enhancers	Fetal Heart	heart
22	chr7:33145600-33147400	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr7:33145600-33147600	Enhancers	Liver	Liver
24	chr7:33145800-33147400	Enhancers	Primary T cells fromperipheralblood	blood
25	chr7:33145800-33147400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr7:33145800-33147600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr7:33145800-33148000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:33146000-33147600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr7:33146200-33147400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:33146200-33147600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:33146400-33147600	Enhancers	Brain Angular Gyrus	brain
32	chr7:33146400-33147600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr7:33146600-33147200	Enhancers	Fetal Stomach	stomach
34	chr7:33146600-33147200	Enhancers	NHLF	lung
35	chr7:33146600-33147400	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr7:33146600-33147600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:33146600-33147600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:33146600-33147600	Enhancers	Brain Substantia Nigra	brain
39	chr7:33146600-33147600	Enhancers	Thymus	Thymus
40	chr7:33146600-33147800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr7:33146600-33148000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:33146800-33147200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:33146800-33147200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:33146800-33147200	Enhancers	Primary hematopoietic stem cells	blood
45	chr7:33146800-33147200	Enhancers	Brain Hippocampus Middle	brain
46	chr7:33146800-33147400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr7:33146800-33147400	Enhancers	Brain Cingulate Gyrus	brain
48	chr7:33146800-33147400	Enhancers	Duodenum Mucosa	Duodenum
49	chr7:33146800-33147400	Enhancers	Fetal Brain Male	brain
50	chr7:33146800-33147400	Enhancers	Fetal Lung	lung

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