Variant report

Variant	rs16843879
Chromosome Location	chr3:136003194-136003195
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135913368..135917347-chr3:136002399..136005146,3	MCF-7	breast:
2	chr3:135968816..135970584-chr3:136001826..136004051,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114054	Chromatin interaction
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10513002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10935178	1.00[CHB][hapmap];0.86[GIH][hapmap];0.84[MKK][hapmap]
rs13067714	0.93[EUR][1000 genomes]
rs16843978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16843991	1.00[CHB][hapmap]
rs17199880	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs17199978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs17265675	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17266364	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs35375192	1.00[CHB][hapmap]
rs3872588	1.00[CHB][hapmap]
rs3913715	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4125861	0.93[EUR][1000 genomes]
rs55654524	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56057807	0.93[EUR][1000 genomes]
rs56095774	0.81[AMR][1000 genomes]
rs56264828	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56336182	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439638	1.00[CHB][hapmap]
rs6439642	1.00[CHB][hapmap]
rs67389407	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67452583	0.90[EUR][1000 genomes]
rs67525027	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67677899	0.93[EUR][1000 genomes]
rs67692166	0.93[EUR][1000 genomes]
rs6769582	0.84[AMR][1000 genomes]
rs6773604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs6776841	1.00[CHB][hapmap]
rs6781817	1.00[CHB][hapmap];0.93[GIH][hapmap]
rs6783337	1.00[CHB][hapmap]
rs67963055	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67971203	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6800570	1.00[CHB][hapmap];0.93[GIH][hapmap];0.84[MKK][hapmap]
rs6804194	1.00[CHB][hapmap]
rs6808143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7625592	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7634492	1.00[CHB][hapmap];0.93[GIH][hapmap]
rs7650075	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7652176	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9833162	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16843879	VCAN	trans	cerebellum	SCAN
rs16843879	TMEM22	cis	cerebellum	SCAN
rs16843879	STAG1	cis	cerebellum	SCAN
rs16843879	IL20RB	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135976200-136012400	Weak transcription	NHLF	lung
3	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
4	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:135981200-136052000	Weak transcription	NH-A	brain
6	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
7	chr3:135982600-136004000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:135996800-136003600	Weak transcription	HMEC	breast
9	chr3:135996800-136016000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:135997000-136004000	Weak transcription	Right Ventricle	heart
11	chr3:135997000-136010600	Weak transcription	Gastric	stomach
12	chr3:135997000-136012000	Weak transcription	Spleen	Spleen
13	chr3:135997400-136015200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:135999600-136004000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:135999600-136005400	Strong transcription	HepG2	liver
17	chr3:135999800-136005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:135999800-136013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:135999800-136013000	Weak transcription	Small Intestine	intestine
20	chr3:135999800-136016200	Weak transcription	Esophagus	oesophagus
21	chr3:135999800-136016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:135999800-136019000	Weak transcription	NHEK	skin
23	chr3:135999800-136038200	Weak transcription	Fetal Brain Male	brain
24	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
25	chr3:136000000-136003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:136000000-136004000	Weak transcription	Fetal Kidney	kidney
27	chr3:136000000-136004000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:136000000-136004000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:136000000-136004000	Weak transcription	Osteobl	bone
30	chr3:136000000-136016600	Weak transcription	Thymus	Thymus
31	chr3:136000000-136024600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:136000200-136004000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:136000200-136008200	Strong transcription	Dnd41	blood
34	chr3:136000200-136012200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:136000200-136038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:136000400-136004000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:136000400-136004000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:136000400-136004000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:136000400-136004000	Weak transcription	A549	lung
40	chr3:136001000-136003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:136001000-136003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:136001200-136003800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:136001200-136004000	Weak transcription	HSMMtube	muscle
44	chr3:136001200-136006200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:136001200-136006800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:136001200-136008200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:136001200-136011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:136001200-136016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:136001200-136019200	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:136001400-136006200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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