Variant report

Variant	rs7518546
Chromosome Location	chr1:150790829-150790830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150784245..150785810-chr1:150789685..150791349,2	MCF-7	breast:
2	chr1:150550706..150553008-chr1:150788888..150791389,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTSK-1	chr1:150790396-150790917	NONHSAT006330

Variant related genes	Relation type
ENSG00000200175	Chromatin interaction
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10788796	1.00[CEU][hapmap]
rs11204728	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1241576	1.00[CEU][hapmap]
rs1415146	1.00[CEU][hapmap]
rs1415147	1.00[AMR][1000 genomes]
rs267727	1.00[CEU][hapmap]
rs267728	1.00[CEU][hapmap]
rs6587519	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6587521	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6587522	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6587534	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6688430	1.00[CEU][hapmap]
rs7515228	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7517945	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7518440	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7533914	1.00[CEU][hapmap]
rs7536645	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv872420	chr1:150786038-150847647	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150765400-150793600	Weak transcription	Fetal Heart	heart
2	chr1:150782200-150791200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:150782200-150791400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:150782200-150795800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:150782200-150809600	Strong transcription	Fetal Muscle Leg	muscle
6	chr1:150782200-150809800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr1:150782200-150813000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:150782400-150812200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr1:150782600-150796600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:150782600-150802800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:150782800-150792800	Strong transcription	Placenta	Placenta
12	chr1:150782800-150795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:150783000-150792600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:150783000-150795800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:150783000-150797000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:150783200-150791200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:150783200-150792000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:150783200-150794000	Strong transcription	HSMM	muscle
19	chr1:150783200-150795800	Strong transcription	NH-A	brain
20	chr1:150783200-150796000	Strong transcription	Adipose Nuclei	Adipose
21	chr1:150783200-150796000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:150783200-150797000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:150783200-150809800	Strong transcription	Fetal Thymus	thymus
24	chr1:150783200-150816600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:150783200-150816800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:150783400-150793400	Strong transcription	Osteobl	bone
27	chr1:150784000-150802000	Strong transcription	Fetal Lung	lung
28	chr1:150784200-150791200	Strong transcription	Fetal Stomach	stomach
29	chr1:150784200-150791400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:150784200-150795000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:150784200-150796000	Strong transcription	Fetal Intestine Large	intestine
32	chr1:150784600-150791200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:150784600-150791200	Strong transcription	Fetal Intestine Small	intestine
34	chr1:150785200-150791200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:150785400-150791200	Strong transcription	Colonic Mucosa	Colon
36	chr1:150785800-150792600	Strong transcription	Liver	Liver
37	chr1:150785800-150793000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:150785800-150793000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:150785800-150793200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:150785800-150806400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:150785800-150812400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:150786000-150791000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:150786000-150793800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:150786000-150796000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:150786000-150808600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:150786800-150793400	Weak transcription	Fetal Kidney	kidney
47	chr1:150786800-150794800	Weak transcription	Gastric	stomach
48	chr1:150788200-150796000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:150788400-150791000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:150788400-150791000	Strong transcription	Skeletal Muscle Male	skeletal muscle

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