Variant report

Variant	rs1420148
Chromosome Location	chr7:33217665-33217666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1009355	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230133	0.81[CHB][hapmap]
rs10250045	0.86[CHB][hapmap]
rs10257361	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10268074	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs10279081	0.86[CHB][hapmap]
rs1030029	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs10951383	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs11763098	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12155105	0.82[CHB][hapmap]
rs12537278	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs12666022	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12671191	0.86[CHB][hapmap]
rs1345308	0.90[CHB][hapmap]
rs1362368	0.86[JPT][hapmap]
rs1362371	0.90[CHB][hapmap]
rs1420158	0.90[CHB][hapmap]
rs1420159	0.90[CHB][hapmap]
rs1548880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1592465	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs1894873	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs2006387	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024430	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs4720115	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs4723261	0.94[CHB][hapmap]
rs4723263	0.90[JPT][hapmap]
rs4723265	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4723272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723273	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6462467	0.86[CHB][hapmap]
rs6950434	0.95[CHB][hapmap]
rs6960483	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6968400	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs721533	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs759396	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764041	0.84[CHB][hapmap]
rs7776834	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7778657	0.86[CHB][hapmap]
rs7779367	0.86[CHB][hapmap]
rs7780194	0.95[CHB][hapmap]
rs7781187	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7783610	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7791710	0.95[CHB][hapmap]
rs7793759	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802888	0.81[CHB][hapmap]
rs964707	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs986553	0.95[CHB][hapmap];0.93[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv830943	chr7:33167106-33352759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1420148	BBS9	cis	lymphoblastoid	seeQTL
rs1420148	BBS9	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33185400-33218000	Weak transcription	Brain Angular Gyrus	brain
2	chr7:33185600-33224000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:33190200-33230400	Weak transcription	Gastric	stomach
4	chr7:33195200-33220200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:33197000-33222200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:33197200-33220400	Weak transcription	Brain Anterior Caudate	brain
7	chr7:33202400-33219800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:33203800-33221200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:33206200-33225400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:33206400-33220200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:33206400-33221200	Weak transcription	Colonic Mucosa	Colon
12	chr7:33206400-33230400	Weak transcription	Right Ventricle	heart
13	chr7:33206600-33217800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:33206600-33222600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr7:33206600-33230400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:33206600-33232600	Weak transcription	Pancreas	Pancrea
17	chr7:33206600-33234800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr7:33206800-33222400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:33206800-33230400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:33210800-33230200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr7:33213400-33230600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:33213600-33218800	Weak transcription	Primary T cells from cord blood	blood
23	chr7:33213800-33218800	Weak transcription	Fetal Intestine Large	intestine
24	chr7:33214000-33230400	Weak transcription	Liver	Liver
25	chr7:33214200-33220200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr7:33214200-33223600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:33214200-33226000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:33214400-33220200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr7:33214400-33220400	Weak transcription	Fetal Brain Female	brain
30	chr7:33214400-33220400	Weak transcription	Psoas Muscle	Psoas
31	chr7:33214400-33221400	Weak transcription	Primary B cells from cord blood	blood
32	chr7:33215000-33222400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr7:33215200-33222200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr7:33215400-33219600	Weak transcription	Dnd41	blood
35	chr7:33215400-33225600	Weak transcription	Osteobl	bone
36	chr7:33215600-33218000	Weak transcription	Lung	lung
37	chr7:33215600-33219000	Weak transcription	Fetal Intestine Small	intestine
38	chr7:33216200-33220200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:33216200-33225600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:33216400-33222000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr7:33216400-33225600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:33217000-33218000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr7:33217000-33218600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:33217000-33219000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr7:33217000-33239200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:33217200-33217800	Strong transcription	Adipose Nuclei	Adipose
47	chr7:33217200-33218000	Strong transcription	Brain Hippocampus Middle	brain
48	chr7:33217200-33218200	Strong transcription	Brain Substantia Nigra	brain
49	chr7:33217200-33219000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr7:33217200-33221000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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