Variant report

Variant	rs16889848
Chromosome Location	chr6:37464724-37464725
allele	C/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:37448778..37451469-chr6:37463694..37466649,2	K562	blood:
2	chr6:37463837..37466464-chr6:37476098..37478071,3	K562	blood:
3	chr6:37391025..37393237-chr6:37463835..37465802,2	K562	blood:
4	chr6:37391025..37394535-chr6:37463764..37466076,3	K562	blood:
5	chr6:37452990..37456369-chr6:37463812..37466534,3	K562	blood:
6	chr6:37463748..37465363-chr6:37527578..37530048,2	K562	blood:
7	chr6:37283647..37285257-chr6:37464011..37465663,2	K562	blood:
8	chr6:37454324..37456090-chr6:37463248..37465258,2	MCF-7	breast:
9	chr6:37283647..37285526-chr6:37464011..37465545,2	K562	blood:
10	chr6:37427824..37429548-chr6:37463570..37465546,2	K562	blood:
11	chr6:37463764..37465711-chr6:37517339..37519147,2	K562	blood:
12	chr6:37458847..37461415-chr6:37462946..37464920,2	MCF-7	breast:
13	chr6:37463658..37465932-chr6:37466196..37468217,2	MCF-7	breast:
14	chr6:37463945..37467008-chr6:37467223..37469909,3	MCF-7	breast:
15	chr6:37438746..37442515-chr6:37463014..37466587,3	K562	blood:
16	chr6:37463721..37466572-chr6:37527557..37531360,4	K562	blood:
17	chr6:37278969..37281772-chr6:37464044..37467373,3	K562	blood:
18	chr6:37402051..37404356-chr6:37464049..37465588,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198937	Chromatin interaction
ENSG00000137200	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12529271	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17572459	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28385585	0.89[AFR][1000 genomes]
rs55738600	0.86[AFR][1000 genomes]
rs55800130	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58351141	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67409335	0.81[EUR][1000 genomes]
rs73427657	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs879482	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs904251	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs914353	0.87[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16889848	NCR2	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37443600-37466600	Weak transcription	A549	lung
2	chr6:37446800-37466600	Weak transcription	Hela-S3	cervix
3	chr6:37447600-37466800	Weak transcription	HSMM	muscle
4	chr6:37448400-37466800	Weak transcription	Stomach Mucosa	stomach
5	chr6:37450200-37467200	Weak transcription	Small Intestine	intestine
6	chr6:37451400-37465600	Weak transcription	Colonic Mucosa	Colon
7	chr6:37451600-37466800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:37451600-37467000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:37451800-37466600	Weak transcription	Primary B cells from cord blood	blood
10	chr6:37451800-37466800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:37452000-37466600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:37452000-37466800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:37452200-37466800	Weak transcription	NHLF	lung
14	chr6:37452600-37466800	Weak transcription	NHDF-Ad	bronchial
15	chr6:37452600-37466800	Weak transcription	Osteobl	bone
16	chr6:37453200-37466600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:37453400-37466800	Weak transcription	Fetal Intestine Large	intestine
18	chr6:37456400-37467000	Weak transcription	Fetal Intestine Small	intestine
19	chr6:37456600-37466800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:37458000-37466200	Weak transcription	Lung	lung
21	chr6:37458000-37466800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:37458200-37466800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:37458400-37466200	Weak transcription	HepG2	liver
24	chr6:37459000-37466800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:37459400-37466600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:37459400-37466800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:37459400-37466800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:37459400-37467000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:37459600-37466600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:37459800-37466600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:37459800-37466800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:37460000-37466600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:37460000-37466600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:37460000-37466800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:37460000-37466800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:37460000-37467000	Weak transcription	Right Atrium	heart
37	chr6:37460400-37465600	Weak transcription	Primary T cells from cord blood	blood
38	chr6:37460400-37466600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:37460400-37466600	Weak transcription	Right Ventricle	heart
40	chr6:37460400-37466800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:37460600-37464800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:37460600-37466600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:37460600-37466600	Weak transcription	Brain Anterior Caudate	brain
44	chr6:37460600-37466600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:37460600-37466600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:37460800-37466600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:37460800-37466800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr6:37461400-37466600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:37461400-37466600	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:37461400-37466800	Weak transcription	Brain Hippocampus Middle	brain

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