Variant report

Variant	rs17138183
Chromosome Location	chr6:4402202-4402203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4401864..4404753-chr6:4405538..4407059,2	MCF-7	breast:
2	chr6:4401718..4402258-chr6:4475763..4476371,2	MCF-7	breast:
3	chr6:4401256..4404324-chr6:4774451..4776953,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153046	Chromatin interaction
ENSG00000236336	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10485314	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195311	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195598	1.00[ASN][1000 genomes]
rs13195767	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13199395	0.91[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202835	1.00[ASN][1000 genomes]
rs13203709	1.00[ASN][1000 genomes]
rs13204463	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204714	1.00[ASN][1000 genomes]
rs13204863	1.00[ASN][1000 genomes]
rs13208005	0.84[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209392	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210174	1.00[ASN][1000 genomes]
rs13210434	1.00[ASN][1000 genomes]
rs13210994	1.00[ASN][1000 genomes]
rs13214243	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214540	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215112	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215125	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218058	1.00[ASN][1000 genomes]
rs13220119	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330790	1.00[ASN][1000 genomes]
rs1330793	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411653	1.00[ASN][1000 genomes]
rs17511568	1.00[ASN][1000 genomes]
rs34971804	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35262147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35364338	1.00[ASN][1000 genomes]
rs4959967	1.00[ASN][1000 genomes]
rs6899991	1.00[ASN][1000 genomes]
rs6901275	1.00[ASN][1000 genomes]
rs6901445	1.00[ASN][1000 genomes]
rs6933015	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937849	1.00[ASN][1000 genomes]
rs6938854	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742092	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744183	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755347	1.00[ASN][1000 genomes]
rs7761922	1.00[ASN][1000 genomes]
rs885182	0.80[EUR][1000 genomes]
rs9392042	0.80[EUR][1000 genomes]
rs9392600	1.00[ASN][1000 genomes]
rs9504097	1.00[ASN][1000 genomes]
rs9504099	1.00[ASN][1000 genomes]
rs9766812	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600861	chr6:4238488-4469641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv462618	chr6:4238488-4472587	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv600862	chr6:4238488-4472587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv949364	chr6:4253413-4466981	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv600863	chr6:4255387-4472587	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1027498	chr6:4255640-4471635	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv2763995	chr6:4255640-4474114	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1020205	chr6:4255640-4474114	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv600864	chr6:4255708-4464630	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv516402	chr6:4255708-4472587	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv462619	chr6:4255708-4472587	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv600865	chr6:4255708-4472587	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv462620	chr6:4255708-4481421	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv600866	chr6:4255708-4481421	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv600867	chr6:4255725-4464630	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv462621	chr6:4255725-4472587	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv600868	chr6:4255725-4472587	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv1029501	chr6:4255745-4471635	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv432845	chr6:4255905-4471472	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv1030655	chr6:4257190-4473701	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv538108	chr6:4257190-4473701	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv1030840	chr6:4257390-4473562	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv538109	chr6:4257390-4473562	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv1026890	chr6:4259075-4471635	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	nsv1030588	chr6:4264933-4455210	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv1021257	chr6:4264933-4473384	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv538110	chr6:4264933-4473384	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv916553	chr6:4269714-4437920	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
29	nsv1016621	chr6:4277411-4473384	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
30	nsv600869	chr6:4294450-4430623	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
31	nsv883413	chr6:4371622-4474114	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv1021743	chr6:4382308-4494308	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
33	nsv538111	chr6:4382308-4494308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	nsv600870	chr6:4391872-4429310	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17138183	SNRNP48	cis	parietal	SCAN
rs17138183	EEF1E1	cis	cerebellum	SCAN
rs17138183	FARS2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4395400-4402600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:4395600-4405800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:4396000-4402400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:4397200-4406800	Enhancers	Fetal Muscle Leg	muscle
5	chr6:4398000-4402400	Weak transcription	Brain Anterior Caudate	brain
6	chr6:4398000-4402800	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:4398600-4402800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:4399400-4402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:4400400-4402400	Weak transcription	Aorta	Aorta
10	chr6:4400600-4402400	Enhancers	A549	lung
11	chr6:4400600-4403000	Enhancers	Fetal Stomach	stomach
12	chr6:4400800-4404200	Enhancers	NHDF-Ad	bronchial
13	chr6:4400800-4404600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:4401200-4403600	Enhancers	Esophagus	oesophagus
15	chr6:4401600-4402600	Enhancers	Fetal Lung	lung
16	chr6:4401800-4402600	Enhancers	Stomach Mucosa	stomach
17	chr6:4401800-4403800	Enhancers	Fetal Muscle Trunk	muscle
18	chr6:4401800-4403800	Enhancers	NHLF	lung
19	chr6:4401800-4404200	Enhancers	Osteobl	bone
20	chr6:4402000-4402400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:4402000-4402400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:4402000-4402400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:4402000-4402600	Enhancers	Spleen	Spleen
24	chr6:4402000-4402800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:4402000-4402800	Enhancers	HSMM	muscle
26	chr6:4402000-4403400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:4402000-4403400	Enhancers	Placenta	Placenta
28	chr6:4402000-4403600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:4402000-4404400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:4402000-4404400	Enhancers	Left Ventricle	heart
31	chr6:4402000-4404600	Enhancers	Right Ventricle	heart
32	chr6:4402000-4405000	Enhancers	HSMMtube	muscle
33	chr6:4402200-4402400	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr6:4402200-4402600	Enhancers	Adipose Nuclei	Adipose
35	chr6:4402200-4403200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:4402200-4403200	Enhancers	Ovary	ovary
37	chr6:4402200-4403200	Enhancers	Pancreas	Pancrea
38	chr6:4402200-4403400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:4402200-4403400	Enhancers	Hela-S3	cervix
40	chr6:4402200-4403600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr6:4402200-4403600	Enhancers	Gastric	stomach
42	chr6:4402200-4403600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr6:4402200-4403800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:4402200-4404000	Enhancers	Psoas Muscle	Psoas
45	chr6:4402200-4404000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr6:4402200-4404800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:4402200-4404800	Enhancers	Brain Substantia Nigra	brain
48	chr6:4402200-4404800	Enhancers	Right Atrium	heart

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