Variant report

Variant	rs1420154
Chromosome Location	chr7:33290931-33290932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:33288330..33291319-chr7:33303929..33306157,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10225173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10251775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10254116	0.91[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10262453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10262890	0.81[EUR][1000 genomes]
rs10271927	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10272438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12155002	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12530700	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12534242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12536300	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12536596	0.84[ASN][1000 genomes]
rs12537512	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12537875	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12538649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1345306	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1420152	0.95[CEU][hapmap];0.93[LWK][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1420153	1.00[ASN][1000 genomes]
rs1590140	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17396870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17724206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1978333	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28435377	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28789535	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3843532	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4720113	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4720114	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4723276	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6946608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6947352	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6979640	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7785463	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7789007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9768604	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv606610	chr7:33218763-33486316	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1016416	chr7:33241443-33559477	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv916660	chr7:33272493-33506384	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1420154	C7orf41	cis	cerebellum	SCAN
rs1420154	NPSR1	cis	parietal	SCAN
rs1420154	BBS9	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33283800-33316000	Weak transcription	Ovary	ovary
2	chr7:33286800-33291600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:33287200-33296000	Weak transcription	Pancreas	Pancrea
4	chr7:33287800-33293600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:33288000-33291200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr7:33288800-33317600	Weak transcription	Gastric	stomach
7	chr7:33289000-33291200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:33289200-33291000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:33289200-33291400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:33289400-33291200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:33289400-33291200	Enhancers	NHDF-Ad	bronchial
12	chr7:33289400-33291200	Enhancers	Osteobl	bone
13	chr7:33289400-33309000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:33289600-33291200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:33289600-33310800	Weak transcription	Psoas Muscle	Psoas
16	chr7:33289800-33291200	Enhancers	Colon Smooth Muscle	Colon
17	chr7:33289800-33291200	Enhancers	NHLF	lung
18	chr7:33290000-33291200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:33290000-33316200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:33290400-33291000	Enhancers	Fetal Muscle Leg	muscle
21	chr7:33290400-33291600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:33290600-33291200	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr7:33290600-33291800	ZNF genes & repeats	Left Ventricle	heart
24	chr7:33290800-33291000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:33290800-33291000	Enhancers	Fetal Kidney	kidney
26	chr7:33290800-33295800	Weak transcription	Fetal Lung	lung
27	chr7:33290800-33309000	Weak transcription	Fetal Stomach	stomach
28	chr7:33290800-33316400	Weak transcription	Aorta	Aorta

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