Variant report

Variant	rs11929668
Chromosome Location	chr3:119535795-119535796
allele	C/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	chr3:119531331..119533784-chr3:119534969..119537956,2	K562	blood:
3	chr3:119531732..119533815-chr3:119534255..119536418,2	MCF-7	breast:
4	chr3:119532575..119536291-chr3:119538231..119540719,3	K562	blood:

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];1.00[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]
rs1054191	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]
rs11918155	1.00[ASN][1000 genomes]
rs11925762	1.00[ASN][1000 genomes]
rs11928653	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
rs11929668	IGSF11	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119529400-119535800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:119529400-119537000	Strong transcription	Fetal Intestine Large	intestine
3	chr3:119529400-119537800	Strong transcription	Fetal Intestine Small	intestine
4	chr3:119529400-119544000	Weak transcription	Right Atrium	heart
5	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:119529600-119536000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:119529600-119543400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
9	chr3:119529800-119543600	Weak transcription	GM12878-XiMat	blood
10	chr3:119530200-119542800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:119531600-119536200	Weak transcription	Fetal Heart	heart
12	chr3:119532000-119543800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:119532400-119535800	Weak transcription	Left Ventricle	heart
14	chr3:119532400-119551000	Weak transcription	Right Ventricle	heart
15	chr3:119533600-119537200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:119534000-119544800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:119534400-119537400	Strong transcription	Liver	Liver
18	chr3:119534600-119536800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:119534800-119558600	Weak transcription	Colonic Mucosa	Colon
20	chr3:119535000-119544200	Weak transcription	HepG2	liver
21	chr3:119535400-119536000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:119535600-119536400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:119535600-119536400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin

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