Variant report

Variant	rs7621788
Chromosome Location	chr3:67628201-67628202
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	chr3:67626314..67629227-chr3:67636253..67638089,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1028952	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12486198	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13069557	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13085475	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17046618	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17046620	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1928565	0.86[CHB][hapmap]
rs2250952	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2634727	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2772452	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2772453	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2772456	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35739416	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4856790	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4856791	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60133628	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6787983	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6794288	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794298	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7622020	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7628362	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7629697	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7636059	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7636075	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7643495	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9680952	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9682288	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9682933	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
2	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7621788	FRMD4B	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67578200-67634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:67579400-67633800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:67579400-67657600	Weak transcription	Pancreas	Pancrea
4	chr3:67582200-67637000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:67594000-67631000	Weak transcription	K562	blood
6	chr3:67595000-67639400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:67596400-67629000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:67598000-67644200	Weak transcription	NHLF	lung
9	chr3:67599600-67629000	Weak transcription	Right Ventricle	heart
10	chr3:67600200-67628800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:67601800-67673000	Weak transcription	Fetal Heart	heart
12	chr3:67602200-67644200	Weak transcription	Gastric	stomach
13	chr3:67602200-67654800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:67602200-67655400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:67602200-67656000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:67602400-67646200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:67602600-67635600	Weak transcription	Aorta	Aorta
18	chr3:67609200-67637000	Weak transcription	Ovary	ovary
19	chr3:67609400-67644000	Weak transcription	NHDF-Ad	bronchial
20	chr3:67612400-67697200	Weak transcription	Hela-S3	cervix
21	chr3:67614000-67658600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:67615000-67628800	Weak transcription	HUVEC	blood vessel
23	chr3:67616600-67644200	Weak transcription	HSMM	muscle
24	chr3:67618600-67655600	Weak transcription	NH-A	brain
25	chr3:67620400-67639800	Weak transcription	Small Intestine	intestine
26	chr3:67621000-67637200	Weak transcription	HepG2	liver
27	chr3:67621200-67644200	Weak transcription	Esophagus	oesophagus
28	chr3:67621200-67657600	Weak transcription	Fetal Stomach	stomach
29	chr3:67621400-67640000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:67621400-67650400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:67621600-67634000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:67621800-67628800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:67621800-67629000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:67621800-67634600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:67621800-67639400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:67621800-67640600	Weak transcription	Placenta	Placenta
37	chr3:67621800-67644000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:67621800-67658000	Weak transcription	Thymus	Thymus
39	chr3:67622000-67628600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:67622000-67628800	Weak transcription	Fetal Lung	lung
41	chr3:67622000-67635600	Weak transcription	GM12878-XiMat	blood
42	chr3:67622000-67640800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:67622000-67641400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:67622000-67648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:67622200-67657400	Weak transcription	Brain Substantia Nigra	brain
46	chr3:67622400-67635800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:67622400-67637000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:67622400-67647800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:67622600-67635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:67622600-67644400	Weak transcription	HMEC	breast

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