Variant report

Variant	rs4652538
Chromosome Location	chr1:180913194-180913195
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	chr1:180913085..180916186-chr1:180922715..180925400,3	MCF-7	breast:
2	chr1:180907561..180909890-chr1:180910550..180913382,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STX6-2	chr1:180913178-180915236	ENSG00000243155.1

Variant related genes	Relation type
ENSG00000232586	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2331995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35607389	1.00[AMR][1000 genomes]
rs944234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180887600-180915800	Weak transcription	Osteobl	bone
2	chr1:180888600-180917200	Weak transcription	Gastric	stomach
3	chr1:180895400-180914200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:180896400-180915400	Weak transcription	HSMMtube	muscle
5	chr1:180896400-180917400	Weak transcription	Fetal Kidney	kidney
6	chr1:180896600-180913400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:180896800-180921800	Weak transcription	Pancreas	Pancrea
8	chr1:180897400-180915400	Weak transcription	HSMM	muscle
9	chr1:180899000-180916600	Strong transcription	Fetal Stomach	stomach
10	chr1:180899000-180920200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr1:180899000-180922600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:180900000-180922800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:180900600-180920000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:180901800-180914000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:180901800-180915200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:180902200-180913600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:180902600-180913600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:180903400-180914400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:180904000-180915400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:180904200-180916200	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:180904400-180915400	Weak transcription	Fetal Brain Male	brain
22	chr1:180904800-180922400	Weak transcription	Colonic Mucosa	Colon
23	chr1:180905200-180919200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:180905400-180918000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:180905400-180922400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:180905400-180940600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:180905800-180913400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:180906200-180919200	Weak transcription	Esophagus	oesophagus
29	chr1:180906400-180913600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:180906600-180913400	Weak transcription	NHLF	lung
31	chr1:180907000-180913600	Weak transcription	Spleen	Spleen
32	chr1:180907200-180913200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:180907200-180913200	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:180907200-180913200	Weak transcription	Dnd41	blood
35	chr1:180907400-180916000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:180907600-180913400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:180907800-180922400	Weak transcription	NHDF-Ad	bronchial
38	chr1:180908000-180913200	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:180908000-180913400	Weak transcription	Brain Angular Gyrus	brain
40	chr1:180908600-180921800	Weak transcription	Right Atrium	heart
41	chr1:180908800-180914000	Weak transcription	Primary T cells from cord blood	blood
42	chr1:180909000-180913400	Weak transcription	Right Ventricle	heart
43	chr1:180909200-180913400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:180909200-180913400	Weak transcription	Fetal Intestine Small	intestine
45	chr1:180909200-180913400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:180909400-180913400	Weak transcription	Brain Germinal Matrix	brain
47	chr1:180909400-180913600	Weak transcription	Thymus	Thymus
48	chr1:180909400-180914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:180909600-180913200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:180909600-180913400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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