Variant report

Variant	rs10896104
Chromosome Location	chr11:66001869-66001870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66000981..66003295-chr11:66025694..66027840,2	MCF-7	breast:
2	chr11:66001119..66003370-chr11:66003822..66006822,3	K562	blood:
3	chr11:65999678..66002038-chr11:66045531..66047368,2	K562	blood:
4	chr11:66001048..66005281-chr11:66024022..66027550,4	K562	blood:

Variant related genes	Relation type
ENSG00000174871	Chromatin interaction
ENSG00000245156	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000174996	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10791865	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1115508	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151537	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1151539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1151540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203798	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1717669	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892939	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508657	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3016319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521109	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs524859	0.87[GIH][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs528842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555360	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555853	0.94[ASN][1000 genomes]
rs556595	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs708471	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs708472	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs801731	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801734	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801735	0.90[EUR][1000 genomes]
rs801736	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801737	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801739	0.95[EUR][1000 genomes]
rs801741	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9326370	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10896104	PACS1	cis	parietal	SCAN
rs10896104	RAB1B	cis	cerebellum	SCAN
rs10896104	C11orf2	cis	parietal	SCAN
rs10896104	SNX32	cis	parietal	SCAN
rs10896104	RAB1B	cis	parietal	SCAN
rs10896104	MRGPRF	cis	parietal	SCAN
rs10896104	KLC2	cis	Muscle Skeletal	GTEx
rs10896104	RP11-867G23.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65961400-66011200	Weak transcription	Psoas Muscle	Psoas
2	chr11:65976600-66006000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:65977400-66010600	Strong transcription	Fetal Stomach	stomach
4	chr11:65977600-66018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:65984600-66024200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:65985800-66017800	Weak transcription	Fetal Heart	heart
7	chr11:65987800-66003400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:65989600-66024200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:65990000-66002600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:65990200-66003000	Weak transcription	HepG2	liver
11	chr11:65990200-66007600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:65990200-66019800	Strong transcription	Primary T cells from cord blood	blood
13	chr11:65990400-66009200	Weak transcription	K562	blood
14	chr11:65990600-66003000	Weak transcription	Fetal Kidney	kidney
15	chr11:65990600-66015800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:65990600-66018400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:65990800-66008600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:65990800-66009200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr11:65990800-66018600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr11:65991000-66015400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:65991200-66012400	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr11:65991200-66018600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:65991200-66018600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:65991600-66008200	Strong transcription	Primary B cells from cord blood	blood
25	chr11:65991600-66012800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:65991600-66018400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:65991600-66018400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:65991800-66004000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:65991800-66005400	Strong transcription	Thymus	Thymus
30	chr11:65991800-66018400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:65992800-66009600	Weak transcription	HUVEC	blood vessel
32	chr11:65993800-66004000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr11:65993800-66018400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr11:65994400-66015200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:65994400-66018600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:65994600-66013200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:65994600-66013800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:65994600-66018600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:65994800-66002800	Strong transcription	NH-A	brain
40	chr11:65995000-66003600	Strong transcription	HSMMtube	muscle
41	chr11:65995000-66018000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:65995000-66018800	Strong transcription	Fetal Intestine Small	intestine
43	chr11:65995200-66003200	Strong transcription	Fetal Muscle Leg	muscle
44	chr11:65995200-66015600	Strong transcription	Lung	lung
45	chr11:65995400-66008000	Strong transcription	Colon Smooth Muscle	Colon
46	chr11:65995600-66012000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:65995800-66008400	Weak transcription	Fetal Brain Male	brain
48	chr11:65996000-66024400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:65996200-66002400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr11:65996600-66011800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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