Variant report

Variant	rs4840157
Chromosome Location	chr6:101326375-101326376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:101326042..101328536-chr6:101641903..101644507,2	K562	blood:
2	chr6:101319726..101322538-chr6:101323434..101327261,5	K562	blood:
3	chr6:101324614..101326514-chr6:101327615..101329304,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112249	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11155708	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11755579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11758174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759127	0.93[JPT][hapmap];0.81[AFR][1000 genomes]
rs12209186	0.95[ASN][1000 genomes]
rs13193416	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13205402	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13212730	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13220881	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17672397	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1813223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2004276	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2398247	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34555037	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34716527	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35748724	0.84[AFR][1000 genomes]
rs4840156	0.81[AFR][1000 genomes]
rs4840159	0.80[EUR][1000 genomes]
rs4840160	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4840161	0.84[AFR][1000 genomes]
rs4840164	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs599934	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs62420689	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62422111	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs652335	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs669543	0.82[ASN][1000 genomes]
rs6917195	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694418	0.82[ASN][1000 genomes]
rs723742	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7758630	0.83[ASN][1000 genomes]
rs9322270	0.86[ASW][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9322271	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9322276	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9322279	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9377236	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9377240	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9386258	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390698	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390701	0.84[AFR][1000 genomes]
rs9390702	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9399695	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399697	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9404059	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9404060	0.86[ASN][1000 genomes]
rs979122	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791225	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs998254	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4840157	LIN28B	cis	parietal	SCAN
rs4840157	ASCC3	cis	cerebellum	SCAN
rs4840157	ASCC3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101269200-101326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:101285600-101326600	Weak transcription	NHLF	lung
3	chr6:101291200-101326400	Weak transcription	Brain Anterior Caudate	brain
4	chr6:101294600-101328600	Weak transcription	Spleen	Spleen
5	chr6:101297000-101327200	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:101297000-101328200	Weak transcription	Ovary	ovary
7	chr6:101300200-101326600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:101300200-101328400	Weak transcription	Esophagus	oesophagus
9	chr6:101300200-101328400	Weak transcription	Lung	lung
10	chr6:101302600-101327800	Weak transcription	Stomach Mucosa	stomach
11	chr6:101304200-101326600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:101304400-101327800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:101305000-101327800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:101309800-101326600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:101311600-101326400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:101311600-101327800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:101311800-101326400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:101311800-101326600	Weak transcription	Pancreas	Pancrea
19	chr6:101311800-101326600	Weak transcription	Thymus	Thymus
20	chr6:101311800-101328200	Weak transcription	Aorta	Aorta
21	chr6:101311800-101328400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:101311800-101328400	Weak transcription	Left Ventricle	heart
23	chr6:101313000-101327200	Weak transcription	Fetal Intestine Large	intestine
24	chr6:101314800-101326400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:101314800-101326800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:101315200-101327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:101315600-101327200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:101315800-101326400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:101315800-101327200	Weak transcription	Adipose Nuclei	Adipose
30	chr6:101315800-101327200	Weak transcription	Placenta	Placenta
31	chr6:101315800-101327800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:101316000-101326400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:101316000-101326400	Weak transcription	Osteobl	bone
34	chr6:101316000-101327000	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:101316000-101327400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr6:101316200-101326400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr6:101316200-101327000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:101316400-101326800	Weak transcription	Primary T cells from cord blood	blood
39	chr6:101316400-101327200	Weak transcription	Fetal Thymus	thymus
40	chr6:101316400-101327200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr6:101316600-101327800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:101317000-101326400	Weak transcription	NHDF-Ad	bronchial
43	chr6:101318800-101327600	Weak transcription	Fetal Lung	lung
44	chr6:101319600-101328600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:101320800-101326400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:101320800-101327600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:101320800-101328200	Weak transcription	Fetal Stomach	stomach
48	chr6:101321000-101326600	Weak transcription	HUVEC	blood vessel
49	chr6:101321000-101327200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr6:101321400-101327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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