Variant report

Variant	rs1054191
Chromosome Location	chr3:119536897-119536898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119529297..119532483-chr3:119535259..119538181,3	MCF-7	breast:
2	chr3:119535902..119537516-chr3:119539010..119541085,2	MCF-7	breast:
3	chr3:119531331..119533784-chr3:119534969..119537956,2	K562	blood:
4	chr3:119533302..119535583-chr3:119535890..119538879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144852	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10511395	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054190	0.85[GIH][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs11918155	1.00[ASN][1000 genomes]
rs11925762	1.00[ASN][1000 genomes]
rs11928653	1.00[ASN][1000 genomes]
rs11929668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314595	0.90[CEU][hapmap];0.86[TSI][hapmap]
rs1579031	0.90[CEU][hapmap]
rs16830076	1.00[ASN][1000 genomes]
rs16830097	1.00[ASN][1000 genomes]
rs1719889	0.90[CEU][hapmap]
rs2037547	0.90[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2461818	1.00[ASN][1000 genomes]
rs4072520	0.90[CEU][hapmap];0.86[TSI][hapmap]
rs55644728	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs55910624	0.80[EUR][1000 genomes]
rs56822345	1.00[ASN][1000 genomes]
rs57450016	1.00[ASN][1000 genomes]
rs60971947	1.00[ASN][1000 genomes]
rs62264684	1.00[ASN][1000 genomes]
rs6438549	1.00[ASN][1000 genomes]
rs66588775	1.00[ASN][1000 genomes]
rs66802265	1.00[ASN][1000 genomes]
rs66858682	1.00[ASN][1000 genomes]
rs6769435	0.90[CEU][hapmap]
rs6770095	1.00[ASN][1000 genomes]
rs6771023	0.90[CEU][hapmap];0.91[MEX][hapmap]
rs6790751	0.90[CEU][hapmap];0.86[TSI][hapmap]
rs73175814	1.00[ASN][1000 genomes]
rs73175826	1.00[ASN][1000 genomes]
rs73175828	0.80[EUR][1000 genomes]
rs73192016	1.00[ASN][1000 genomes]
rs73192035	1.00[ASN][1000 genomes]
rs73192043	1.00[ASN][1000 genomes]
rs7617372	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs7620750	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs7624540	0.90[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs7638068	1.00[ASN][1000 genomes]
rs7638261	1.00[ASN][1000 genomes]
rs9829763	0.90[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs9879992	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1054191	IGSF11	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119529400-119537000	Strong transcription	Fetal Intestine Large	intestine
2	chr3:119529400-119537800	Strong transcription	Fetal Intestine Small	intestine
3	chr3:119529400-119544000	Weak transcription	Right Atrium	heart
4	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:119529600-119543400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
7	chr3:119529800-119543600	Weak transcription	GM12878-XiMat	blood
8	chr3:119530200-119542800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:119532000-119543800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:119532400-119551000	Weak transcription	Right Ventricle	heart
11	chr3:119533600-119537200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr3:119534000-119544800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:119534400-119537400	Strong transcription	Liver	Liver
14	chr3:119534800-119558600	Weak transcription	Colonic Mucosa	Colon
15	chr3:119535000-119544200	Weak transcription	HepG2	liver
16	chr3:119536000-119537000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:119536000-119543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:119536200-119537200	Enhancers	Fetal Heart	heart
19	chr3:119536200-119543000	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:119536200-119569000	Weak transcription	Esophagus	oesophagus
21	chr3:119536400-119537000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr3:119536400-119543200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:119536400-119543400	Weak transcription	HMEC	breast
24	chr3:119536400-119545600	Weak transcription	Left Ventricle	heart
25	chr3:119536400-119570200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:119536600-119537400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:119536600-119543400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:119536600-119543800	Weak transcription	HSMMtube	muscle
29	chr3:119536600-119576000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:119536600-119576400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:119536800-119537000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:119536800-119543200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:119536800-119543600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:119536800-119543600	Weak transcription	HSMM	muscle

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