Variant report

Variant	rs6789958
Chromosome Location	chr3:142413407-142413408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142409223..142411101-chr3:142411877..142413945,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11715610	0.80[CEU][hapmap]
rs12695767	0.84[EUR][1000 genomes]
rs12695768	0.90[EUR][1000 genomes]
rs13058771	0.90[EUR][1000 genomes]
rs13069113	0.90[EUR][1000 genomes]
rs13079246	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13080785	0.90[EUR][1000 genomes]
rs13100985	0.89[EUR][1000 genomes]
rs1357530	0.88[CEU][hapmap]
rs16852486	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17623267	0.90[EUR][1000 genomes]
rs1983434	0.88[CEU][hapmap]
rs2012010	0.90[EUR][1000 genomes]
rs2030613	0.88[CEU][hapmap]
rs2049325	0.88[CEU][hapmap]
rs2140432	0.88[CEU][hapmap]
rs2227928	0.80[CEU][hapmap]
rs2354175	0.90[EUR][1000 genomes]
rs2883380	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3736560	0.90[EUR][1000 genomes]
rs3736561	0.90[EUR][1000 genomes]
rs4413348	0.88[CEU][hapmap]
rs4683688	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4683689	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4683690	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6440089	0.80[CEU][hapmap]
rs6440094	0.81[CEU][hapmap]
rs6440098	0.88[CEU][hapmap]
rs6440102	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6775813	0.88[CEU][hapmap]
rs6782400	0.80[CEU][hapmap]
rs6784361	0.90[EUR][1000 genomes]
rs6785894	0.91[EUR][1000 genomes]
rs6792259	0.81[CEU][hapmap]
rs6793735	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6798232	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6799752	0.81[CEU][hapmap]
rs6808205	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6808302	0.90[EUR][1000 genomes]
rs7430429	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7610557	0.81[CEU][hapmap]
rs7615316	0.88[CEU][hapmap]
rs7631313	0.88[CEU][hapmap]
rs7648354	0.80[CEU][hapmap]
rs7651071	0.81[CEU][hapmap]
rs940211	0.90[EUR][1000 genomes]
rs940212	0.90[EUR][1000 genomes]
rs9832606	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9862919	0.86[CEU][hapmap]
rs9866958	0.88[CEU][hapmap]
rs9869842	0.80[CEU][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	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142385800-142415400	Weak transcription	A549	lung
3	chr3:142389200-142414800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:142392800-142418000	Weak transcription	HepG2	liver
6	chr3:142392800-142425400	Weak transcription	Dnd41	blood
7	chr3:142392800-142433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:142393000-142426000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:142393400-142426200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:142404200-142418000	Weak transcription	HMEC	breast
11	chr3:142404600-142416200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:142407200-142417000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:142408800-142430400	Weak transcription	Liver	Liver
14	chr3:142411800-142413600	Enhancers	NHEK	skin
15	chr3:142412800-142416600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:142412800-142426600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:142413200-142422600	Weak transcription	Duodenum Mucosa	Duodenum

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