Variant report

Variant	rs2762357
Chromosome Location	chr6:25506398-25506399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25498087..25500839-chr6:25503392..25507019,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10456322	0.82[EUR][1000 genomes]
rs10456323	0.82[EUR][1000 genomes]
rs12192331	0.81[EUR][1000 genomes]
rs12192342	0.82[EUR][1000 genomes]
rs12207791	0.82[EUR][1000 genomes]
rs150533	0.83[EUR][1000 genomes]
rs184202	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs212927	0.83[EUR][1000 genomes]
rs212931	0.83[EUR][1000 genomes]
rs212932	0.83[EUR][1000 genomes]
rs212937	0.83[EUR][1000 genomes]
rs212940	0.83[EUR][1000 genomes]
rs301377	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs301388	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3827502	0.82[EUR][1000 genomes]
rs4097270	0.89[ASN][1000 genomes]
rs441472	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs443641	0.86[EUR][1000 genomes]
rs485567	0.83[EUR][1000 genomes]
rs56383372	0.83[EUR][1000 genomes]
rs6927384	0.81[EUR][1000 genomes]
rs6931843	0.82[EUR][1000 genomes]
rs72839082	0.82[EUR][1000 genomes]
rs72839085	0.81[EUR][1000 genomes]
rs72839087	0.82[EUR][1000 genomes]
rs72839088	0.81[EUR][1000 genomes]
rs7742338	0.82[EUR][1000 genomes]
rs9348685	0.82[EUR][1000 genomes]

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	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv10468	chr6:25506093-25519529	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2762357	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25449400-25515800	Weak transcription	Lung	lung
2	chr6:25456400-25515800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:25456400-25537000	Weak transcription	Esophagus	oesophagus
4	chr6:25463200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:25464200-25518400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:25466400-25516000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:25466800-25515800	Weak transcription	Fetal Stomach	stomach
8	chr6:25471600-25597200	Weak transcription	Gastric	stomach
9	chr6:25473600-25516000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:25480000-25511400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:25480800-25523600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:25483000-25532200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:25484800-25515600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:25490400-25515800	Weak transcription	Thymus	Thymus
15	chr6:25490400-25521800	Weak transcription	GM12878-XiMat	blood
16	chr6:25490400-25543000	Weak transcription	Hela-S3	cervix
17	chr6:25490600-25524600	Weak transcription	A549	lung
18	chr6:25490800-25506400	Weak transcription	Fetal Intestine Small	intestine
19	chr6:25490800-25511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:25490800-25515800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:25490800-25515800	Weak transcription	Ovary	ovary
22	chr6:25490800-25516400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:25490800-25521400	Weak transcription	Small Intestine	intestine
24	chr6:25491600-25521000	Weak transcription	HSMMtube	muscle
25	chr6:25494000-25515400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:25494000-25515600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:25494000-25551400	Weak transcription	Left Ventricle	heart
28	chr6:25494600-25515600	Weak transcription	Fetal Thymus	thymus
29	chr6:25495000-25515800	Weak transcription	Fetal Lung	lung
30	chr6:25495000-25516400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:25498000-25515800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:25500400-25511000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:25500400-25515800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:25500400-25515800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:25500400-25516000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:25500600-25515800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:25500600-25516000	Weak transcription	HMEC	breast
38	chr6:25500600-25516400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:25500600-25520800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:25500600-25523800	Weak transcription	Placenta	Placenta
41	chr6:25500800-25509000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:25500800-25511200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:25500800-25516000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:25501800-25515200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:25502000-25515800	Weak transcription	Fetal Intestine Large	intestine
46	chr6:25503400-25506800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:25503400-25506800	Enhancers	NHEK	skin
48	chr6:25504000-25518000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:25504200-25512800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:25504400-25506800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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