Variant report

Variant	rs1127894
Chromosome Location	chr11:66335548-66335549
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66335068-66335674	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr11:66335460-66335610	WERI-Rb-1	eye:	n/a	n/a
3	HMGN3	chr11:66335471-66336214	K562	blood:	n/a	n/a
4	MXI1	chr11:66335373-66336534	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr11:66335440-66335590	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr11:66335440-66335590	HRPEpiC	eye:	n/a	n/a
7	MAZ	chr11:66335399-66336387	IMR90	lung:	n/a	chr11:66336123-66336132 chr11:66336121-66336130 chr11:66336122-66336129
8	CTCF	chr11:66335420-66335570	HBMEC	blood vessel:	n/a	n/a
9	CTCF	chr11:66335480-66335630	SK-N-SH_RA	brain:	n/a	n/a
10	ZBTB7A	chr11:66335483-66336119	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66333517..66336306-chr11:66404884..66407774,3	K562	blood:
2	chr11:66333502..66336819-chr11:66382812..66384536,3	K562	blood:
3	chr11:66334662..66337726-chr11:66444588..66447609,3	K562	blood:
4	chr11:66333502..66335839-chr11:66382927..66384488,2	K562	blood:
5	chr11:66333513..66337489-chr11:66382854..66385992,4	MCF-7	breast:
6	chr11:66333833..66336382-chr11:66443152..66446114,2	MCF-7	breast:

Variant related genes	Relation type
CTSF	TF binding region
ENSG00000239306	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000173933	Chromatin interaction
ENSG00000173914	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10791882	0.85[ASN][1000 genomes]
rs1671064	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1815739	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2000939	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3018318	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs486584	0.85[ASN][1000 genomes]
rs509556	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs531490	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs540874	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs545009	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs560556	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs572846	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs615205	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs618838	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs630021	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs677488	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs678397	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv3376183	chr11:66334601-66337149	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1127894	CCS	cis	multi-tissue	Pritchard
rs1127894	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs1127894	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs1127894	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66329400-66336600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr11:66330400-66335600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:66330400-66337800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:66330600-66336800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:66330800-66336000	Weak transcription	Fetal Lung	lung
7	chr11:66331000-66335600	Weak transcription	Aorta	Aorta
8	chr11:66331200-66336600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:66331400-66337800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:66331600-66337800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:66332000-66335600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:66332000-66336600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:66333600-66335600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:66334600-66336000	Enhancers	Fetal Brain Male	brain
15	chr11:66334800-66335600	Flanking Active TSS	Brain Angular Gyrus	brain
16	chr11:66334800-66335600	Flanking Active TSS	Fetal Brain Female	brain
17	chr11:66334800-66335600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr11:66334800-66336400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:66335000-66335600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr11:66335000-66335600	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr11:66335000-66335600	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr11:66335000-66335600	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr11:66335000-66335600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr11:66335000-66335800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:66335000-66335800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr11:66335000-66335800	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr11:66335000-66336200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr11:66335000-66336200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:66335000-66336600	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr11:66335200-66335600	Enhancers	Primary hematopoietic stem cells	blood
31	chr11:66335200-66335600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:66335200-66335600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:66335200-66335600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr11:66335200-66335600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:66335200-66335600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr11:66335200-66335600	Flanking Active TSS	Ovary	ovary
37	chr11:66335200-66335600	Flanking Active TSS	Rectal Smooth Muscle	rectum
38	chr11:66335200-66335600	Flanking Active TSS	NHDF-Ad	bronchial
39	chr11:66335200-66335800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:66335200-66335800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:66335200-66335800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr11:66335200-66336000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:66335200-66336000	Enhancers	Fetal Heart	heart
44	chr11:66335200-66336000	Flanking Active TSS	Spleen	Spleen
45	chr11:66335200-66336200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:66335200-66336200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:66335200-66336200	Active TSS	Colon Smooth Muscle	Colon
48	chr11:66335200-66336400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr11:66335200-66336400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:66335200-66336400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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