Variant report

Variant	rs4661175
Chromosome Location	chr1:155931368-155931369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155920875..155922518-chr1:155929901..155931540,2	MCF-7	breast:
2	chr1:155929776..155931816-chr1:155936198..155938525,2	MCF-7	breast:
3	chr1:155902649..155906864-chr1:155928278..155934368,7	MCF-7	breast:
4	chr1:155903455..155906976-chr1:155930050..155931967,4	K562	blood:
5	chr1:155911063..155912721-chr1:155931066..155933374,2	MCF-7	breast:
6	chr1:155910241..155913815-chr1:155925549..155931886,5	K562	blood:
7	chr1:155929665..155932692-chr1:155935407..155940311,5	MCF-7	breast:
8	chr1:155903455..155906976-chr1:155930050..155931967,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173080	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10796955	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11264422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11585845	0.93[ASW][hapmap]
rs12024880	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12027412	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12563627	0.85[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1749405	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs1889532	0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1889533	0.86[ASN][1000 genomes]
rs2993207	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3856261	0.88[JPT][hapmap]
rs4661151	0.85[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4661217	0.84[ASN][1000 genomes]
rs4661218	0.86[ASW][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs488079	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs490498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs539602	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61813286	0.87[ASN][1000 genomes]
rs625658	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs639398	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs656247	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs656737	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6670493	0.84[ASN][1000 genomes]
rs670523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs729022	0.85[ASW][hapmap];0.88[CEU][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap]
rs7534858	0.86[ASW][hapmap]
rs7538214	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs822478	0.89[JPT][hapmap]
rs822490	0.87[MEX][hapmap]
rs822504	0.86[EUR][1000 genomes]
rs822505	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs822508	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap]
rs860295	0.87[MEX][hapmap]
rs928596	0.86[ASW][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4661175	YY1AP1	cis	cerebellum	SCAN
rs4661175	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs4661175	RIT1	cis	cerebellum	SCAN
rs4661175	SLC39A1	cis	cerebellum	SCAN
rs4661175	ROBLD3	cis	parietal	SCAN
rs4661175	FAM189B	cis	cerebellum	SCAN
rs4661175	RIT1	cis	Thyroid	GTEx
rs4661175	SPRR3	cis	parietal	SCAN
rs4661175	PRUNE	cis	cerebellum	SCAN
rs4661175	UBQLN4	trans	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155911200-155940000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155914800-155931600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:155915200-155936800	Strong transcription	Fetal Brain Female	brain
5	chr1:155915200-155937000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:155915800-155931600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:155915800-155935200	Strong transcription	Brain Germinal Matrix	brain
8	chr1:155915800-155936600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:155916000-155931400	Strong transcription	HUVEC	blood vessel
10	chr1:155916000-155937000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:155916200-155931600	Weak transcription	Right Atrium	heart
12	chr1:155916200-155932400	Strong transcription	Colon Smooth Muscle	Colon
13	chr1:155916200-155937000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:155916400-155931800	Strong transcription	Lung	lung
15	chr1:155916400-155936200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:155916400-155936400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:155916400-155936600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:155916400-155937200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:155916400-155937400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:155916600-155932400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:155916600-155935800	Strong transcription	Fetal Intestine Small	intestine
22	chr1:155916600-155937000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:155916600-155937200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:155916800-155931600	Strong transcription	Colonic Mucosa	Colon
25	chr1:155916800-155932400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:155916800-155937000	Strong transcription	Thymus	Thymus
27	chr1:155917000-155931800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:155917000-155937200	Strong transcription	Fetal Intestine Large	intestine
29	chr1:155917000-155939400	Strong transcription	Dnd41	blood
30	chr1:155917200-155936800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:155917400-155931600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:155917400-155931800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:155917600-155932000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:155917600-155936400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:155917600-155937000	Strong transcription	Fetal Thymus	thymus
36	chr1:155917800-155932200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:155917800-155933200	Strong transcription	Rectal Smooth Muscle	rectum
38	chr1:155917800-155936400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:155918000-155931400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:155918000-155936000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:155918000-155936000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:155918400-155935000	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:155919600-155936400	Strong transcription	Primary T cells from cord blood	blood
44	chr1:155920400-155931800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:155922200-155931800	Weak transcription	Psoas Muscle	Psoas
46	chr1:155924000-155937200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:155926200-155931600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:155926400-155937200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:155926600-155932600	Strong transcription	Small Intestine	intestine
50	chr1:155926800-155932600	Strong transcription	K562	blood

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