Variant report

Variant	rs10896135
Chromosome Location	chr11:66551002-66551003
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66511430..66516575-chr11:66550719..66554900,5	MCF-7	breast:
2	chr11:66550222..66552472-chr11:66552736..66554855,2	K562	blood:
3	chr11:66548712..66551794-chr11:66555818..66557613,3	MCF-7	breast:
4	chr11:66485898..66488789-chr11:66548912..66551207,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173715	Chromatin interaction
ENSG00000173898	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10160758	0.94[CEU][hapmap]
rs10750790	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10791889	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10791890	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10791891	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10791892	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896139	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11227610	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11600959	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2077432	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2167457	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2187041	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741194	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3741364	1.00[JPT][hapmap]
rs4576826	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930184	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4930390	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6591222	0.94[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7103627	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7119426	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7120256	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs714766	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7570	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7930203	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7948839	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs9971487	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription 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	70 gene(s)	inside rSNPs	diseases
6	nsv516087	chr11:66516049-66579572	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv508638	chr11:66541653-66643634	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bipolar disorder	21926972	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10896135	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs10896135	CTSF	cis	Whole Blood	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66513200-66555000	Weak transcription	Pancreas	Pancrea
2	chr11:66513400-66606800	Weak transcription	Brain Angular Gyrus	brain
3	chr11:66527000-66574200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:66527000-66595600	Weak transcription	HSMM	muscle
5	chr11:66527400-66571600	Weak transcription	Primary T cells from cord blood	blood
6	chr11:66530000-66559000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:66530000-66571400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:66530000-66605400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:66530200-66556000	Weak transcription	Gastric	stomach
10	chr11:66530200-66582400	Weak transcription	HUVEC	blood vessel
11	chr11:66530600-66551200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:66530600-66555800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:66530600-66575200	Weak transcription	Esophagus	oesophagus
14	chr11:66530600-66600000	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:66530800-66581800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:66531000-66572800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:66531200-66577800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:66531400-66555200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:66531400-66555800	Weak transcription	Fetal Intestine Small	intestine
20	chr11:66531400-66557000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:66531400-66578000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:66531800-66569400	Weak transcription	Brain Germinal Matrix	brain
23	chr11:66532000-66568400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:66532200-66555800	Weak transcription	Fetal Stomach	stomach
25	chr11:66532400-66555600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr11:66534200-66555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:66534400-66555400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:66535600-66555400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:66535600-66556200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:66536600-66555400	Weak transcription	A549	lung
31	chr11:66536600-66572000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:66536800-66556000	Weak transcription	NHEK	skin
33	chr11:66536800-66558200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:66538200-66575800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:66539800-66571400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:66540000-66556400	Weak transcription	Primary B cells from cord blood	blood
37	chr11:66540200-66556200	Weak transcription	Thymus	Thymus
38	chr11:66544000-66609600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:66548400-66571400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr11:66548800-66557800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr11:66550200-66555400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:66550200-66555600	Weak transcription	Fetal Thymus	thymus
43	chr11:66550400-66555600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:66550400-66571400	Weak transcription	Fetal Brain Female	brain
45	chr11:66550800-66556000	Weak transcription	Placenta	Placenta
46	chr11:66551000-66555600	Weak transcription	Hela-S3	cervix

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