Variant report

Variant	rs34541797
Chromosome Location	chr6:146205304-146205305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:146204410..146206507-chr6:146211730..146213654,2	MCF-7	breast:
2	chr6:146054912..146058368-chr6:146203943..146209352,13	MCF-7	breast:
3	chr6:146187673..146189565-chr6:146204450..146206308,2	K562	blood:
4	chr6:146054628..146056452-chr6:146203586..146205795,3	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRM1-1	chr6:146204341-146207721	NONHSAT115401
2	lnc-GRM1-1	chr6:146204341-146207721	NONHSAT115402
3	lnc-GRM1-1	chr6:146204341-146207721	ENSG00000235652.3
4	lnc-GRM1-1	chr6:146204341-146207721	NONHSAT115397

No data

Variant related genes	Relation type
ENSG00000270828	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000112425	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1884364	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1890170	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1970306	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2142978	0.82[ASN][1000 genomes]
rs2142980	0.91[ASN][1000 genomes]
rs2206142	0.82[ASN][1000 genomes]
rs2223411	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2235481	0.85[ASN][1000 genomes]
rs2246132	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2253757	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265470	0.86[ASN][1000 genomes]
rs2265475	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2485631	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2777485	0.80[ASN][1000 genomes]
rs62435775	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6570732	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6900175	0.80[ASN][1000 genomes]
rs6912351	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702322	0.82[ASN][1000 genomes]
rs7746618	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7753273	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9285508	0.87[ASN][1000 genomes]
rs9376965	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9386136	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9390374	0.82[ASN][1000 genomes]
rs9485017	0.83[ASN][1000 genomes]
rs9497403	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9497426	0.84[ASN][1000 genomes]
rs960385	0.82[ASN][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	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146185200-146212200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:146186400-146213200	Weak transcription	Brain Anterior Caudate	brain
3	chr6:146188000-146218800	Weak transcription	Right Ventricle	heart
4	chr6:146188800-146209000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr6:146189400-146214400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:146189600-146211800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:146193400-146207600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:146194000-146211800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:146194800-146212400	Weak transcription	HUVEC	blood vessel
10	chr6:146195000-146209400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:146196200-146210000	Weak transcription	Fetal Brain Male	brain
12	chr6:146196600-146212200	Weak transcription	Aorta	Aorta
13	chr6:146196600-146219600	Weak transcription	HMEC	breast
14	chr6:146196800-146209000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:146197200-146209000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:146197800-146219600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:146198000-146209400	Weak transcription	Brain Substantia Nigra	brain
18	chr6:146198000-146209600	Weak transcription	Fetal Brain Female	brain
19	chr6:146198200-146212400	Weak transcription	Fetal Kidney	kidney
20	chr6:146198200-146218600	Weak transcription	Fetal Heart	heart
21	chr6:146198200-146225600	Weak transcription	HSMMtube	muscle
22	chr6:146198800-146207200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:146199200-146208800	Weak transcription	Fetal Thymus	thymus
24	chr6:146199600-146209400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:146199800-146209200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:146199800-146209600	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:146199800-146214400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:146200000-146209600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:146200000-146214200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:146200200-146209000	Weak transcription	Placenta	Placenta
31	chr6:146200400-146207400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:146200400-146209000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:146200400-146228600	Weak transcription	Pancreas	Pancrea
34	chr6:146200600-146207800	Weak transcription	Osteobl	bone
35	chr6:146200600-146209600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:146200600-146211000	Weak transcription	Brain Angular Gyrus	brain
37	chr6:146200600-146212200	Weak transcription	NHDF-Ad	bronchial
38	chr6:146200800-146208800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:146200800-146209600	Weak transcription	Brain Germinal Matrix	brain
40	chr6:146200800-146209800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:146200800-146213400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:146201000-146207800	Weak transcription	Fetal Intestine Large	intestine
43	chr6:146201000-146209600	Weak transcription	Esophagus	oesophagus
44	chr6:146201000-146209600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:146201000-146209800	Weak transcription	NH-A	brain
46	chr6:146201000-146210200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:146201200-146206600	Weak transcription	Fetal Lung	lung
48	chr6:146201200-146208800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:146201200-146211200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:146201200-146217400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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