Variant report

Variant	rs4659221
Chromosome Location	chr1:120168353-120168354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120162586..120166440-chr1:120167182..120171199,5	K562	blood:
2	chr1:120166768..120169738-chr1:120190505..120193186,2	MCF-7	breast:
3	chr1:120167579..120169748-chr1:120230698..120233512,2	K562	blood:
4	chr1:120166833..120169520-chr1:120180162..120182281,2	K562	blood:
5	chr1:120165887..120168379-chr1:120172138..120174819,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1045827	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10754416	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10802123	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10802124	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10802126	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10923879	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12024934	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12064265	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12067843	0.98[ASN][1000 genomes]
rs12076924	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12079724	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2281493	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748711	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3795662	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3795663	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850870	0.93[ASN][1000 genomes]
rs3862260	0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3862261	0.93[ASN][1000 genomes]
rs3862262	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4079793	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4659218	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4659219	0.93[ASN][1000 genomes]
rs699775	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552885	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4659221	NBPF7	cis	parietal	SCAN
rs4659221	HSD3B2	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120154800-120173600	Weak transcription	Brain Anterior Caudate	brain
2	chr1:120156800-120169800	Weak transcription	NHDF-Ad	bronchial
3	chr1:120156800-120173800	Weak transcription	Colonic Mucosa	Colon
4	chr1:120158400-120169800	Weak transcription	NH-A	brain
5	chr1:120161000-120170200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:120161200-120168600	Strong transcription	Placenta	Placenta
7	chr1:120161400-120169200	Weak transcription	Psoas Muscle	Psoas
8	chr1:120161400-120169200	Weak transcription	Small Intestine	intestine
9	chr1:120161400-120169600	Weak transcription	HSMMtube	muscle
10	chr1:120161400-120169800	Weak transcription	Right Atrium	heart
11	chr1:120161600-120171600	Weak transcription	HSMM	muscle
12	chr1:120162200-120174400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:120162200-120174600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:120163600-120168600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:120163600-120188400	Weak transcription	Hela-S3	cervix
16	chr1:120163800-120168800	Strong transcription	Osteobl	bone
17	chr1:120164000-120169400	Strong transcription	NHEK	skin
18	chr1:120164200-120168600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:120164200-120168600	Strong transcription	Fetal Lung	lung
20	chr1:120164400-120168800	Strong transcription	Fetal Intestine Small	intestine
21	chr1:120164400-120169400	Strong transcription	Fetal Stomach	stomach
22	chr1:120164400-120171000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:120164600-120168600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:120164600-120169200	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:120164800-120168400	Strong transcription	Ovary	ovary
26	chr1:120164800-120168400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:120164800-120168800	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr1:120164800-120168800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:120164800-120169000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:120164800-120169000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:120164800-120169400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:120165000-120168400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:120165000-120168400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:120165000-120168400	Strong transcription	Fetal Brain Female	brain
35	chr1:120165000-120168600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:120165000-120168600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:120165000-120168600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:120165000-120168600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:120165000-120168600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr1:120165000-120168800	Strong transcription	Lung	lung
41	chr1:120165000-120169000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:120165200-120168400	Strong transcription	Right Ventricle	heart
43	chr1:120165200-120168600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:120165200-120168600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:120165200-120168600	Strong transcription	Colon Smooth Muscle	Colon
46	chr1:120165200-120168600	Strong transcription	Left Ventricle	heart
47	chr1:120165200-120169000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:120165400-120168400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:120165400-120168600	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr1:120165400-120168600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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