Variant report

Variant	rs16881929
Chromosome Location	chr7:33042945-33042946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10486518	1.00[ASW][hapmap]
rs12113707	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12667900	0.94[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap]
rs12668520	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16881927	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17170045	1.00[ASW][hapmap]
rs17471162	1.00[ASW][hapmap]
rs2953608	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4723231	0.84[EUR][1000 genomes]
rs4723239	1.00[ASW][hapmap]
rs6963198	0.93[ASN][1000 genomes]
rs6965006	0.84[ASN][1000 genomes]
rs6976843	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7782137	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs7786711	0.83[EUR][1000 genomes];0.96[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	esv14217	chr7:32999213-33053044	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16881929	BBS9	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33003800-33064200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:33004400-33043800	Weak transcription	Esophagus	oesophagus
3	chr7:33012200-33056400	Weak transcription	Fetal Kidney	kidney
4	chr7:33012600-33077600	Weak transcription	Psoas Muscle	Psoas
5	chr7:33015200-33053200	Weak transcription	Brain Anterior Caudate	brain
6	chr7:33016200-33043800	Weak transcription	Right Ventricle	heart
7	chr7:33017400-33045000	Weak transcription	Liver	Liver
8	chr7:33019400-33045000	Weak transcription	A549	lung
9	chr7:33020400-33052800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:33024000-33064400	Weak transcription	Brain Angular Gyrus	brain
11	chr7:33026400-33052800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:33026800-33046200	Weak transcription	Spleen	Spleen
13	chr7:33037800-33052200	Weak transcription	Fetal Brain Female	brain
14	chr7:33038200-33052800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:33038200-33055000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:33038200-33080800	Weak transcription	Fetal Brain Male	brain
17	chr7:33038400-33044800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr7:33038400-33051800	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:33038600-33051200	Weak transcription	HSMM	muscle
20	chr7:33038600-33051400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr7:33038600-33052000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:33038600-33053000	Weak transcription	HMEC	breast
23	chr7:33038800-33044400	Weak transcription	HSMMtube	muscle
24	chr7:33038800-33044400	Weak transcription	Osteobl	bone
25	chr7:33038800-33048000	Weak transcription	Dnd41	blood
26	chr7:33038800-33051000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:33038800-33051200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:33038800-33051200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:33038800-33051800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:33038800-33051800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:33038800-33052800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr7:33038800-33052800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:33038800-33052800	Weak transcription	Colonic Mucosa	Colon
34	chr7:33038800-33053000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:33038800-33053000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:33038800-33054800	Weak transcription	NH-A	brain
37	chr7:33039000-33052200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr7:33039000-33052400	Weak transcription	NHLF	lung
39	chr7:33039000-33052600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr7:33039000-33053000	Weak transcription	NHDF-Ad	bronchial
41	chr7:33039200-33044800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:33039200-33049800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:33039200-33065000	Weak transcription	Brain Germinal Matrix	brain
44	chr7:33039400-33044400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr7:33039400-33049600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr7:33039400-33052000	Weak transcription	Fetal Heart	heart
47	chr7:33039400-33052000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:33039400-33052600	Weak transcription	Fetal Lung	lung
49	chr7:33039400-33052800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr7:33039400-33052800	Weak transcription	Stomach Mucosa	stomach

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