Variant report

Variant	rs12668520
Chromosome Location	chr7:33075248-33075249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:33074098..33076234-chr7:33080334..33083060,3	K562	blood:
2	chr7:32981284..32982799-chr7:33074781..33076751,2	MCF-7	breast:
3	chr7:33072862..33075361-chr7:33079989..33082160,2	K562	blood:

Variant related genes	Relation type
ENSG00000122643	Chromatin interaction
ENSG00000205763	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12113707	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12667900	0.80[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap]
rs16881927	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16881929	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2953608	0.82[ASN][1000 genomes]
rs4723231	0.88[EUR][1000 genomes]
rs6963198	0.86[ASN][1000 genomes]
rs6965006	0.85[ASN][1000 genomes]
rs6976843	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7782137	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7786711	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[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	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	esv3478254	chr7:32956181-33133477	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	esv3478255	chr7:32956181-33133477	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv3528603	chr7:32956254-33133429	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	esv3528604	chr7:32956254-33133429	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	esv3366191	chr7:32956659-33134592	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	esv3418466	chr7:32968130-33138898	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12668520	BBS9	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33012600-33077600	Weak transcription	Psoas Muscle	Psoas
2	chr7:33038200-33080800	Weak transcription	Fetal Brain Male	brain
3	chr7:33042600-33083200	Weak transcription	Small Intestine	intestine
4	chr7:33052400-33078200	Weak transcription	Fetal Heart	heart
5	chr7:33053400-33077600	Weak transcription	Brain Substantia Nigra	brain
6	chr7:33053800-33077400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:33055200-33075800	Weak transcription	Spleen	Spleen
8	chr7:33055200-33078200	Weak transcription	NHEK	skin
9	chr7:33055200-33078400	Weak transcription	HMEC	breast
10	chr7:33055200-33083200	Weak transcription	Fetal Brain Female	brain
11	chr7:33056200-33080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:33056200-33083200	Weak transcription	Gastric	stomach
13	chr7:33056200-33083200	Weak transcription	Pancreas	Pancrea
14	chr7:33056800-33078800	Weak transcription	Fetal Kidney	kidney
15	chr7:33057400-33077400	Weak transcription	Brain Anterior Caudate	brain
16	chr7:33057600-33079200	Weak transcription	Placenta	Placenta
17	chr7:33057800-33078400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr7:33060600-33077400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:33060600-33078400	Weak transcription	Ovary	ovary
20	chr7:33061000-33077200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:33062400-33084000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:33062800-33079200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr7:33064200-33077400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr7:33064200-33078000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:33064400-33077200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:33064400-33077400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:33064600-33077200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr7:33065000-33077400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr7:33065600-33077800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:33065800-33075800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:33065800-33077600	Weak transcription	Adipose Nuclei	Adipose
32	chr7:33065800-33077600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr7:33066000-33077400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:33066200-33076000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr7:33066200-33101600	Weak transcription	Lung	lung
36	chr7:33066400-33078400	Weak transcription	Fetal Thymus	thymus
37	chr7:33066600-33079000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:33066800-33100800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:33067000-33077600	Weak transcription	Liver	Liver
40	chr7:33067000-33078200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:33067000-33078200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:33067000-33079000	Weak transcription	Fetal Muscle Leg	muscle
43	chr7:33067000-33079600	Weak transcription	Left Ventricle	heart
44	chr7:33068400-33077400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:33069200-33078400	Weak transcription	Fetal Lung	lung
46	chr7:33069600-33077400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:33069600-33077800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:33069600-33078400	Weak transcription	Aorta	Aorta
49	chr7:33069600-33083200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:33069800-33077800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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