Variant report

Variant	rs2147374
Chromosome Location	chr6:4013741-4013742
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	chr6:4006763..4009757-chr6:4011766..4014574,3	K562	blood:
2	chr6:4008961..4014281-chr6:4016436..4019625,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf146-1	chr6:4006806-4020323	NONHSAT107264

Variant related genes	Relation type
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11754326	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11754413	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11759303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198921	0.95[JPT][hapmap]
rs12662057	0.82[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs17137442	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17137470	0.91[YRI][hapmap]
rs1969836	0.93[ASN][1000 genomes]
rs1969837	0.94[ASN][1000 genomes]
rs28889078	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62394163	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9392546	0.95[ASN][1000 genomes]
rs9405217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9405693	0.82[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1800199	chr6:3986611-4014872	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3991400-4016800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:3991600-4017200	Weak transcription	Fetal Brain Female	brain
3	chr6:3991600-4017400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:3991600-4017600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:3991800-4016600	Weak transcription	Aorta	Aorta
6	chr6:3991800-4017400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:3991800-4017400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:3991800-4017600	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:3997400-4016200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:3997400-4017400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:3997600-4017600	Weak transcription	Psoas Muscle	Psoas
12	chr6:3998000-4017400	Weak transcription	NHLF	lung
13	chr6:3998200-4017400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:3998400-4016200	Weak transcription	Brain Germinal Matrix	brain
15	chr6:3998400-4017600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:3998400-4017600	Weak transcription	Small Intestine	intestine
17	chr6:3998800-4017400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:4000200-4017400	Weak transcription	HUVEC	blood vessel
19	chr6:4001400-4016000	Weak transcription	Hela-S3	cervix
20	chr6:4004400-4016200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:4005000-4016200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:4005600-4017400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:4007400-4013800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:4008400-4017600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:4008600-4016200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:4008600-4017400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:4008600-4017600	Weak transcription	HSMMtube	muscle
28	chr6:4008800-4016200	Weak transcription	Brain Substantia Nigra	brain
29	chr6:4008800-4016200	Weak transcription	NHDF-Ad	bronchial
30	chr6:4008800-4016400	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:4008800-4016600	Weak transcription	Fetal Stomach	stomach
32	chr6:4008800-4017200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr6:4008800-4017400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:4008800-4017400	Weak transcription	Brain Anterior Caudate	brain
35	chr6:4008800-4017400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:4008800-4017400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:4008800-4017400	Weak transcription	Stomach Mucosa	stomach
38	chr6:4008800-4017400	Weak transcription	A549	lung
39	chr6:4009000-4014400	Weak transcription	Fetal Intestine Large	intestine
40	chr6:4009000-4017400	Weak transcription	NH-A	brain
41	chr6:4009000-4017400	Weak transcription	Osteobl	bone
42	chr6:4010000-4015200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr6:4010400-4016400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr6:4011200-4018000	Weak transcription	Pancreas	Pancrea
45	chr6:4011200-4018200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:4011400-4013800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr6:4011400-4013800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:4011400-4014000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:4011400-4014000	Weak transcription	Thymus	Thymus
50	chr6:4011400-4014200	Weak transcription	Fetal Intestine Small	intestine

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