Variant report

Variant	rs17024167
Chromosome Location	chr1:120282232-120282233
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	chr1:120188673..120191126-chr1:120281749..120284526,2	K562	blood:

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12121219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12123085	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12142268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17186233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17258425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4391705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4659019	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4659233	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs512854	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs56239558	0.82[EUR][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	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17024167	C1orf161	cis	parietal	SCAN
rs17024167	CD2	cis	parietal	SCAN
rs17024167	SPAG17	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
2	chr1:120257000-120282400	Weak transcription	A549	lung
3	chr1:120257200-120287000	Weak transcription	NH-A	brain
4	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:120260400-120287600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:120261000-120287200	Strong transcription	Hela-S3	cervix
7	chr1:120261600-120288200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:120261800-120287000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:120261800-120287600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:120262000-120284600	Strong transcription	Fetal Stomach	stomach
11	chr1:120262000-120287200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:120262000-120287400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:120262000-120287400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:120262000-120287800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:120262000-120288200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:120262200-120284400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:120262400-120283600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:120262400-120285000	Strong transcription	NHEK	skin
19	chr1:120262400-120287400	Strong transcription	Dnd41	blood
20	chr1:120262400-120288200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:120262600-120282800	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr1:120262600-120283800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:120263200-120286400	Strong transcription	Thymus	Thymus
24	chr1:120263400-120286800	Strong transcription	Primary T cells from cord blood	blood
25	chr1:120263400-120287400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:120263400-120291400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:120264000-120283800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:120266200-120282600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:120267200-120286800	Weak transcription	Primary B cells from cord blood	blood
30	chr1:120269800-120286800	Weak transcription	Small Intestine	intestine
31	chr1:120271000-120286600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:120271200-120286200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:120272800-120285200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:120274000-120286400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:120275200-120284800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:120275200-120286800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:120275400-120284400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:120275600-120285000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:120275800-120286200	Strong transcription	HepG2	liver
40	chr1:120276400-120285200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:120276400-120285800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:120278600-120287000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:120279000-120284800	Weak transcription	Osteobl	bone
44	chr1:120279200-120286600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:120279200-120290600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:120279400-120284200	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:120279600-120282600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:120279600-120284400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:120279800-120284800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:120280200-120286600	Weak transcription	Rectal Mucosa Donor 31	rectum

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