Variant report

Variant	rs10896112
Chromosome Location	chr11:66116836-66116837
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66116649-66116837	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:66116822-66116947	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:66116394-66116995	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:66114321-66116968	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66108426..66118730-chr11:66133678..66141000,25	MCF-7	breast:
2	chr11:66054499..66057435-chr11:66115136..66117035,2	MCF-7	breast:
3	chr11:66103854..66118324-chr11:66119048..66141728,55	K562	blood:
4	chr11:66115381..66116970-chr11:66233175..66235277,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-867G23.8.1-3	chr11:66116806-66116941	NONHSAT022292

No data

Variant related genes	Relation type
BRMS1	TF binding region
B3GNT1	TF binding region
ENSG00000174851	Chromatin interaction
ENSG00000174669	Chromatin interaction
ENSG00000174547	Chromatin interaction
ENSG00000174516	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1039594	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1047029	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10750784	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10791869	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791872	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10791874	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10791876	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896111	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896115	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896116	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11227465	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11601396	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11823140	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12416747	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12576293	0.81[ASN][1000 genomes]
rs12576299	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12577196	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12577917	0.81[JPT][hapmap]
rs12785321	0.86[EUR][1000 genomes]
rs12785651	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12786563	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12794121	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546358	0.88[EUR][1000 genomes]
rs1784029	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs1785633	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1785639	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1892940	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236679	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279861	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282530	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282531	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3016767	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3177514	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34043951	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4244813	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4466842	0.88[CEU][hapmap]
rs4930177	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930178	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930179	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4930181	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4930360	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4930362	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4930363	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4930366	0.86[EUR][1000 genomes]
rs4930368	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55998145	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56123976	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56321771	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61891449	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6591213	1.00[CEU][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6591215	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6591217	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66810040	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7104253	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7104570	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7105015	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7105401	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7107191	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7110944	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117630	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7126018	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73489638	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7938676	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7939111	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7940980	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs905770	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs947978	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv897781	chr11:66095967-66116911	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv897782	chr11:66099222-66116911	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv897783	chr11:66107527-66118676	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv897784	chr11:66111901-66123043	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv897785	chr11:66112574-66123043	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10896112	RIN1	cis	Whole Blood	GTEx
rs10896112	RP11-867G23.12	cis	Whole Blood	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66115600-66117000	Enhancers	Spleen	Spleen
2	chr11:66115800-66117000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:66115800-66117000	Flanking Active TSS	Fetal Intestine Small	intestine
4	chr11:66115800-66117000	Flanking Active TSS	Hela-S3	cervix
5	chr11:66115800-66117000	Flanking Active TSS	HepG2	liver
6	chr11:66115800-66123400	Weak transcription	Ovary	ovary
7	chr11:66116000-66117000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:66116000-66117000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr11:66116000-66117000	Enhancers	Fetal Brain Male	brain
10	chr11:66116000-66117000	Enhancers	Pancreas	Pancrea
11	chr11:66116000-66118600	Enhancers	Liver	Liver
12	chr11:66116000-66118600	Weak transcription	A549	lung
13	chr11:66116000-66121200	Weak transcription	Primary T cells from cord blood	blood
14	chr11:66116000-66121200	Weak transcription	Thymus	Thymus
15	chr11:66116000-66127200	Weak transcription	Gastric	stomach
16	chr11:66116000-66129400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:66116000-66129600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:66116000-66129600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:66116000-66134400	Weak transcription	Left Ventricle	heart
20	chr11:66116000-66135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:66116000-66137200	Weak transcription	Fetal Kidney	kidney
22	chr11:66116000-66138400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:66116000-66138400	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:66116000-66138400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:66116000-66138400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:66116200-66117000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:66116200-66117000	Enhancers	Brain Germinal Matrix	brain
28	chr11:66116200-66117000	Enhancers	Fetal Brain Female	brain
29	chr11:66116200-66117000	Enhancers	Fetal Stomach	stomach
30	chr11:66116200-66117000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr11:66116200-66117000	Enhancers	Dnd41	blood
32	chr11:66116200-66120800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:66116200-66121000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:66116200-66121200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:66116200-66121200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:66116200-66121200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:66116200-66121400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:66116200-66121800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:66116200-66123400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:66116200-66127000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr11:66116200-66128800	Weak transcription	Fetal Muscle Leg	muscle
42	chr11:66116200-66128800	Weak transcription	Fetal Thymus	thymus
43	chr11:66116200-66129200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:66116200-66129200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:66116200-66129600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:66116200-66129600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr11:66116200-66129800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:66116200-66130000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:66116200-66130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr11:66116200-66137000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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