Variant report

Variant	rs7552885
Chromosome Location	chr1:120164966-120164967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120161786..120164966-chr1:120184691..120189749,4	K562	blood:
2	chr1:120162586..120166440-chr1:120167182..120171199,5	K562	blood:
3	chr1:120145059..120147660-chr1:120162749..120165475,2	MCF-7	breast:
4	chr1:120162086..120165079-chr1:120173514..120175556,2	MCF-7	breast:
5	chr1:120161786..120164966-chr1:120187188..120189749,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1045827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754415	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10754416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802120	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10802123	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10802124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802126	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10923878	0.85[AMR][1000 genomes]
rs10923879	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024934	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12064265	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12067843	0.94[ASN][1000 genomes]
rs12076924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079724	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795662	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795663	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3850870	0.99[ASN][1000 genomes]
rs3862260	0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3862261	0.99[ASN][1000 genomes]
rs3862262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4079793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4659218	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4659219	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4659221	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656016	0.84[JPT][hapmap]
rs699775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	nsv547621	chr1:120164303-120167887	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3428692	chr1:120164454-120167402	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv547622	chr1:120164966-120166681	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7552885	HSD3B2	cis	cerebellum	SCAN
rs7552885	NBPF7	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120146200-120165000	Weak transcription	Aorta	Aorta
2	chr1:120152200-120167800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:120154400-120167400	Weak transcription	Brain Substantia Nigra	brain
4	chr1:120154600-120165000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:120154600-120165000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:120154600-120165000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:120154800-120165000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:120154800-120165200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:120154800-120165400	Weak transcription	Fetal Brain Male	brain
10	chr1:120154800-120173600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:120156800-120165400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:120156800-120169800	Weak transcription	NHDF-Ad	bronchial
13	chr1:120156800-120173800	Weak transcription	Colonic Mucosa	Colon
14	chr1:120157200-120165000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:120157200-120165200	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:120157200-120165400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:120157400-120167800	Weak transcription	Fetal Kidney	kidney
18	chr1:120158400-120169800	Weak transcription	NH-A	brain
19	chr1:120159800-120165000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:120159800-120165200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr1:120159800-120165400	Weak transcription	GM12878-XiMat	blood
22	chr1:120159800-120166600	Weak transcription	K562	blood
23	chr1:120161000-120165200	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:120161000-120170200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:120161200-120165200	Weak transcription	Gastric	stomach
26	chr1:120161200-120165200	Weak transcription	Right Ventricle	heart
27	chr1:120161200-120165400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:120161200-120165400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:120161200-120168600	Strong transcription	Placenta	Placenta
30	chr1:120161400-120165000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:120161400-120165000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:120161400-120165200	Weak transcription	Adipose Nuclei	Adipose
33	chr1:120161400-120165200	Weak transcription	Brain Angular Gyrus	brain
34	chr1:120161400-120169200	Weak transcription	Psoas Muscle	Psoas
35	chr1:120161400-120169200	Weak transcription	Small Intestine	intestine
36	chr1:120161400-120169600	Weak transcription	HSMMtube	muscle
37	chr1:120161400-120169800	Weak transcription	Right Atrium	heart
38	chr1:120161600-120165000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:120161600-120165000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:120161600-120165000	Weak transcription	Lung	lung
41	chr1:120161600-120165200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:120161600-120165200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:120161600-120165200	Weak transcription	Left Ventricle	heart
44	chr1:120161600-120165200	Weak transcription	Pancreas	Pancrea
45	chr1:120161600-120171600	Weak transcription	HSMM	muscle
46	chr1:120161800-120165000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:120161800-120165000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:120162200-120174400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:120162200-120174600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:120162600-120167600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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