Variant report

Variant	rs16862676
Chromosome Location	chr3:150178939-150178940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150161437..150164361-chr3:150177482..150180288,2	K562	blood:
2	chr3:150086925..150089531-chr3:150177059..150179337,2	K562	blood:
3	chr3:150177406..150179513-chr3:150187577..150189487,2	MCF-7	breast:
4	chr3:150169139..150170858-chr3:150178413..150180525,2	MCF-7	breast:
5	chr3:150124596..150127596-chr3:150177344..150180987,4	MCF-7	breast:
6	chr3:150125422..150129437-chr3:150175835..150179595,4	K562	blood:
7	chr3:150124105..150129008-chr3:150174357..150179992,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10513373	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10513374	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10935800	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12639090	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1584586	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs16862627	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs16862644	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868672	0.81[JPT][hapmap]
rs2868425	0.86[JPT][hapmap]
rs4423794	0.85[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4488863	0.87[ASN][1000 genomes]
rs4681204	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4681205	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4681207	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4681616	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4681617	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681618	0.82[JPT][hapmap]
rs59793956	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61483057	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6770424	0.82[JPT][hapmap]
rs6795124	0.81[ASN][1000 genomes]
rs73163692	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73165707	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9784335	0.86[JPT][hapmap]
rs9826729	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9882777	0.86[JPT][hapmap]

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	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150144200-150179000	Weak transcription	Aorta	Aorta
2	chr3:150165600-150187200	Weak transcription	Small Intestine	intestine
3	chr3:150166000-150186200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:150166400-150185600	Weak transcription	Lung	lung
5	chr3:150172000-150184800	Weak transcription	Brain Substantia Nigra	brain
6	chr3:150172200-150179800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:150172400-150179000	Weak transcription	Psoas Muscle	Psoas
8	chr3:150172600-150191600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:150173400-150181000	Weak transcription	Fetal Heart	heart
10	chr3:150173800-150186400	Weak transcription	Colonic Mucosa	Colon
11	chr3:150174400-150179000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:150174400-150179400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:150174600-150179200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:150174600-150186400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:150174800-150179200	Strong transcription	NHDF-Ad	bronchial
16	chr3:150175000-150179000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:150175000-150179000	Strong transcription	Osteobl	bone
18	chr3:150175000-150179400	Strong transcription	Primary B cells from cord blood	blood
19	chr3:150175000-150179600	Weak transcription	Fetal Brain Male	brain
20	chr3:150175000-150179600	Strong transcription	HSMM	muscle
21	chr3:150175000-150184200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:150175200-150179000	Strong transcription	Fetal Thymus	thymus
23	chr3:150175200-150179000	Strong transcription	HSMMtube	muscle
24	chr3:150176000-150180400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:150176400-150182200	Weak transcription	Fetal Stomach	stomach
26	chr3:150176600-150186400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:150176600-150187000	Weak transcription	Fetal Intestine Small	intestine
28	chr3:150176800-150179000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:150176800-150179200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:150176800-150180000	Weak transcription	Gastric	stomach
31	chr3:150176800-150180000	Weak transcription	Spleen	Spleen
32	chr3:150176800-150180600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:150176800-150180600	Weak transcription	GM12878-XiMat	blood
34	chr3:150176800-150180800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:150176800-150183000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:150176800-150183200	Weak transcription	Ovary	ovary
37	chr3:150176800-150183600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:150176800-150183600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:150176800-150184400	Weak transcription	Fetal Brain Female	brain
40	chr3:150176800-150185000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:150176800-150185000	Weak transcription	NHEK	skin
42	chr3:150176800-150186400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:150176800-150186800	Weak transcription	Primary T cells from cord blood	blood
44	chr3:150176800-150187000	Weak transcription	Fetal Intestine Large	intestine
45	chr3:150176800-150187000	Weak transcription	Left Ventricle	heart
46	chr3:150176800-150187000	Weak transcription	Pancreas	Pancrea
47	chr3:150176800-150187000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:150176800-150187200	Weak transcription	Brain Anterior Caudate	brain
49	chr3:150176800-150187200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:150176800-150187200	Weak transcription	Fetal Muscle Leg	muscle

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