Variant report

Variant	rs6541380
Chromosome Location	chr1:93920417-93920418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93913146..93916521-chr1:93916633..93921176,6	K562	blood:
2	chr1:93919359..93921378-chr1:93922417..93924785,2	MCF-7	breast:
3	chr1:93912180..93916451-chr1:93917036..93921176,6	K562	blood:

Variant related genes	Relation type
ENSG00000137942	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12563504	0.83[EUR][1000 genomes]
rs12566373	0.88[EUR][1000 genomes]
rs17110076	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2295330	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs236266	1.00[CEU][hapmap]
rs236295	1.00[CEU][hapmap]
rs236296	1.00[CEU][hapmap]
rs35115771	0.83[EUR][1000 genomes]
rs3754189	0.94[EUR][1000 genomes]
rs3767973	0.81[EUR][1000 genomes]
rs3767979	1.00[CEU][hapmap]
rs3767991	1.00[CEU][hapmap]
rs41292649	0.86[EUR][1000 genomes]
rs57012808	0.81[EUR][1000 genomes]
rs57466479	0.81[EUR][1000 genomes]
rs57914444	0.81[EUR][1000 genomes]
rs59777284	0.81[EUR][1000 genomes]
rs6674143	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6699020	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7524368	0.81[EUR][1000 genomes]
rs7546785	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93915200-93922000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:93915200-93922200	Weak transcription	Gastric	stomach
3	chr1:93915200-93923800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:93915200-93926800	Weak transcription	Pancreas	Pancrea
5	chr1:93915200-93927800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:93915200-93928600	Weak transcription	Ovary	ovary
7	chr1:93915200-93929600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:93915200-93929800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:93915200-93935800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:93915200-93937000	Weak transcription	Esophagus	oesophagus
11	chr1:93915200-93937000	Weak transcription	Lung	lung
12	chr1:93915400-93920800	Weak transcription	Right Atrium	heart
13	chr1:93915400-93922400	Weak transcription	Fetal Stomach	stomach
14	chr1:93915400-93924600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:93915400-93926600	Weak transcription	Liver	Liver
16	chr1:93915400-93926800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:93915400-93926800	Weak transcription	Psoas Muscle	Psoas
18	chr1:93915400-93929800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:93915400-93931000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:93916000-93922400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:93916400-93923800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:93916400-93924600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:93916400-93926600	Weak transcription	Primary B cells from cord blood	blood
24	chr1:93916400-93934800	Weak transcription	Fetal Intestine Large	intestine
25	chr1:93916600-93923800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:93916600-93925600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:93916600-93926000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:93916800-93920800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:93916800-93921000	Weak transcription	Fetal Brain Female	brain
30	chr1:93916800-93922200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:93916800-93922600	Weak transcription	Fetal Lung	lung
32	chr1:93916800-93925600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:93916800-93929400	Weak transcription	Brain Germinal Matrix	brain
34	chr1:93916800-93930400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:93916800-93932800	Weak transcription	Fetal Kidney	kidney
36	chr1:93917400-93922000	Weak transcription	Fetal Intestine Small	intestine
37	chr1:93917600-93920800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:93917600-93937200	Weak transcription	Fetal Brain Male	brain
39	chr1:93918200-93928800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:93919000-93921400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:93919600-93920800	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:93919600-93921200	Enhancers	Right Ventricle	heart
43	chr1:93919800-93921600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:93919800-93922200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:93919800-93922400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:93919800-93922600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:93919800-93923800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:93919800-93937000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:93920000-93921200	Enhancers	HUVEC	blood vessel
50	chr1:93920000-93922000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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