Variant report

No.	Distal block	Cell Line	Cell type
1	chr3:160396356..160398268-chr3:160398713..160401566,2	MCF-7	breast:
2	chr3:160392050..160395141-chr3:160395142..160398552,4	K562	blood:
3	chr3:160395173..160398062-chr3:160414143..160415987,2	K562	blood:
4	chr3:160395405..160397806-chr3:160539467..160541973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207084	Chromatin interaction
ENSG00000179674	Chromatin interaction

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10460866	0.94[EUR][1000 genomes]
rs11720693	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12639488	0.87[CEU][hapmap]
rs13062928	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs13072556	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13075424	0.91[EUR][1000 genomes]
rs13085507	0.96[EUR][1000 genomes]
rs1403045	0.84[CEU][hapmap]
rs16831337	0.85[CEU][hapmap]
rs1879797	0.87[CEU][hapmap]
rs1882125	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs2367209	0.88[EUR][1000 genomes]
rs34058107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34444753	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35498840	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4133253	0.85[CEU][hapmap]
rs57718211	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60339919	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792943	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6806755	0.84[CEU][hapmap]
rs71314011	0.94[EUR][1000 genomes]
rs7610939	0.84[CEU][hapmap]
rs7634255	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7633839	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160394800-160397800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:160395000-160398000	Active TSS	Duodenum Mucosa	Duodenum
3	chr3:160395200-160397800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:160395600-160397800	Enhancers	Hela-S3	cervix
5	chr3:160395600-160401600	Weak transcription	Gastric	stomach
6	chr3:160395600-160401800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:160395800-160400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:160397000-160398600	Enhancers	Fetal Intestine Large	intestine
9	chr3:160397000-160412800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:160397200-160397800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:160397200-160401800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:160397400-160397800	Weak transcription	Stomach Mucosa	stomach
13	chr3:160397400-160399000	Enhancers	Fetal Intestine Small	intestine
14	chr3:160397400-160400800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:160397400-160401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:160397400-160401600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:160397400-160401800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:160397400-160403000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:160397600-160398000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr3:160397600-160401800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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