Variant report

Variant	rs11264342
Chromosome Location	chr1:153711268-153711269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153699587..153702399-chr1:153710970..153713011,3	MCF-7	breast:
2	chr1:153710268..153712803-chr1:153735091..153737564,2	K562	blood:
3	chr1:153707222..153708852-chr1:153709093..153711861,2	K562	blood:

Variant related genes	Relation type
ENSG00000143624	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11583874	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4518941	0.84[EUR][1000 genomes]
rs6427183	0.94[ASN][1000 genomes]
rs6677628	0.82[ASN][1000 genomes]
rs6698058	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs67091466	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541193	0.89[ASW][hapmap];0.85[LWK][hapmap];0.91[YRI][hapmap]
rs7550138	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7552428	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9426875	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
10	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
13	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
14	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
17	nsv1002328	chr1:153672031-153718746	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Active TSS 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	23 gene(s)	inside rSNPs	diseases
18	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
19	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11264342	LCE1B	cis	parietal	SCAN
rs11264342	S100A9	cis	parietal	SCAN
rs11264342	S100A13	cis	parietal	SCAN
rs11264342	SLC27A3	cis	cerebellum	SCAN
rs11264342	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs11264342	S100A13	cis	lymphoblastoid	seeQTL
rs11264342	S100A2	cis	cerebellum	SCAN
rs11264342	S100A16	cis	cerebellum	SCAN
rs11264342	S100A10	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153701200-153716200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:153701400-153712400	Weak transcription	Ovary	ovary
3	chr1:153701600-153712800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:153701800-153711400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:153701800-153712800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:153701800-153713000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:153701800-153713200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:153702000-153711600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:153702000-153712800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:153702000-153712800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:153702000-153713000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:153702000-153713000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:153702000-153713000	Weak transcription	HSMM	muscle
14	chr1:153702000-153713000	Weak transcription	NH-A	brain
15	chr1:153702000-153713000	Weak transcription	NHEK	skin
16	chr1:153702000-153713200	Weak transcription	Gastric	stomach
17	chr1:153702000-153713200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:153702000-153713800	Weak transcription	Esophagus	oesophagus
19	chr1:153702200-153711800	Weak transcription	Lung	lung
20	chr1:153702200-153713000	Weak transcription	Left Ventricle	heart
21	chr1:153702400-153712800	Weak transcription	Brain Substantia Nigra	brain
22	chr1:153702400-153713200	Weak transcription	Colonic Mucosa	Colon
23	chr1:153702600-153712600	Weak transcription	Fetal Thymus	thymus
24	chr1:153702600-153712800	Weak transcription	Fetal Brain Female	brain
25	chr1:153702600-153713000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:153702600-153713000	Weak transcription	Pancreas	Pancrea
27	chr1:153702600-153713000	Weak transcription	HMEC	breast
28	chr1:153702600-153713000	Weak transcription	HSMMtube	muscle
29	chr1:153702600-153713800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:153702600-153714000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:153702800-153711400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:153702800-153712600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:153702800-153712800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:153702800-153712800	Weak transcription	NHLF	lung
35	chr1:153702800-153713000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:153702800-153713000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:153703000-153713000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:153703000-153713800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:153703000-153715800	Weak transcription	Psoas Muscle	Psoas
40	chr1:153703200-153712800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:153703200-153712800	Weak transcription	Brain Germinal Matrix	brain
42	chr1:153703200-153712800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:153703200-153713000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:153703200-153713000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:153703200-153713200	Weak transcription	HUVEC	blood vessel
46	chr1:153703400-153713000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:153703600-153713000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:153703600-153713000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:153703600-153713000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:153703600-153713000	Weak transcription	K562	blood

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