Variant report

Variant	rs11555520
Chromosome Location	chr1:85743452-85743453
allele	C/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	chr1:85740468-85743570	PANC-1	pancreas:	n/a	n/a
2	FOXA1	chr1:85743432-85743794	HepG2	liver:	n/a	chr1:85743641-85743656 chr1:85743665-85743680
3	FOXA1	chr1:85743380-85743937	HepG2	liver:	n/a	chr1:85743641-85743656 chr1:85743665-85743680
4	FOXA1	chr1:85743447-85743762	T-47D	breast:	n/a	chr1:85743641-85743656 chr1:85743665-85743680

No.	Distal block	Cell Line	Cell type
1	chr1:85742187..85745018-chr1:85749555..85753087,3	K562	blood:
2	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
3	chr1:85722628..85726570-chr1:85740869..85744448,4	MCF-7	breast:
4	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
5	chr1:85665227..85667257-chr1:85740935..85743875,2	K562	blood:
6	chr1:85741905..85744580-chr1:85747619..85751624,6	K562	blood:
7	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYR61-3	chr1:85743324-85743771	NONHSAT004241

Variant related genes	Relation type
BCL10	TF binding region
ENSG00000153904	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000162642	Chromatin interaction
ENSG00000264380	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11576939	0.87[CEU][hapmap]
rs4949928	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11555520	CLCA3P	cis	parietal	SCAN
rs11555520	SSX2IP	cis	lymphoblastoid	seeQTL
rs11555520	C1orf52	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742200-85744600	Weak transcription	Gastric	stomach
2	chr1:85742200-85744800	Weak transcription	Spleen	Spleen
3	chr1:85742800-85744400	Weak transcription	Small Intestine	intestine
4	chr1:85742800-85744600	Weak transcription	Pancreas	Pancrea
5	chr1:85742800-85744600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:85742800-85744600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:85742800-85763000	Weak transcription	Ovary	ovary
8	chr1:85743000-85743800	Enhancers	Fetal Heart	heart
9	chr1:85743000-85744200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:85743000-85744200	Weak transcription	Adipose Nuclei	Adipose
11	chr1:85743000-85744400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:85743000-85744400	Weak transcription	HSMM	muscle
13	chr1:85743000-85744400	Weak transcription	HSMMtube	muscle
14	chr1:85743000-85744400	Weak transcription	K562	blood
15	chr1:85743000-85744400	Weak transcription	NHLF	lung
16	chr1:85743000-85744600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:85743000-85744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:85743000-85744600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:85743000-85744600	Weak transcription	Fetal Kidney	kidney
20	chr1:85743000-85744600	Enhancers	HUVEC	blood vessel
21	chr1:85743000-85744800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:85743000-85745400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:85743000-85746000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:85743000-85747400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:85743000-85749200	Weak transcription	Fetal Stomach	stomach
26	chr1:85743000-85749200	Weak transcription	Psoas Muscle	Psoas
27	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
28	chr1:85743200-85743600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:85743200-85743600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:85743200-85743600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:85743200-85744000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:85743200-85744000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:85743200-85744000	Enhancers	HepG2	liver
34	chr1:85743200-85744200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:85743200-85744200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:85743200-85744200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:85743200-85744200	Weak transcription	Fetal Intestine Small	intestine
38	chr1:85743200-85744400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:85743200-85744400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:85743200-85744400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:85743200-85744400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:85743200-85744400	Weak transcription	Liver	Liver
43	chr1:85743200-85744400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:85743200-85744400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:85743200-85744400	Weak transcription	Stomach Mucosa	stomach
46	chr1:85743200-85744400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr1:85743200-85744400	Weak transcription	NH-A	brain
48	chr1:85743200-85744400	Weak transcription	NHDF-Ad	bronchial
49	chr1:85743200-85744400	Weak transcription	Osteobl	bone
50	chr1:85743200-85744600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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