Variant report

Variant	rs6601690
Chromosome Location	chr8:8173255-8173256
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	chr8:8170459..8174320-chr8:8242480..8245231,3	MCF-7	breast:
2	chr8:8145925..8147772-chr8:8172599..8174671,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182319	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11776196	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12549973	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13269488	0.85[ASN][1000 genomes]
rs13276576	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13281575	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1401389	0.86[ASN][1000 genomes]
rs4840923	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62496020	0.82[ASN][1000 genomes]
rs6996347	0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7011400	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs867757	0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915915	chr8:7239471-8222024	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	76 gene(s)	inside rSNPs	diseases
2	nsv533299	chr8:7268825-8222024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	75 gene(s)	inside rSNPs	diseases
3	nsv869874	chr8:7753583-8229906	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
4	nsv817196	chr8:8079861-8255544	Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv465448	chr8:8098079-8403142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription 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	16 gene(s)	inside rSNPs	diseases
7	nsv610152	chr8:8098079-8403142	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv610154	chr8:8101641-8328101	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1032259	chr8:8108863-8247113	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1020290	chr8:8108863-8260280	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv539440	chr8:8108863-8260280	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv1029268	chr8:8130629-8403435	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv539446	chr8:8130629-8403435	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
17	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
18	nsv610156	chr8:8163243-8207339	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6601690	C8orf12	cis	cerebellum	SCAN
rs6601690	MCPH1	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8163400-8174000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:8164400-8174600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr8:8167600-8173800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr8:8167600-8174600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr8:8167800-8174600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr8:8167800-8175600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:8168200-8175600	Weak transcription	Spleen	Spleen
8	chr8:8168200-8175800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:8168400-8174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:8168400-8175400	Weak transcription	Colonic Mucosa	Colon
11	chr8:8168400-8175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr8:8168400-8180600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr8:8168600-8174400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr8:8168600-8174600	Weak transcription	Ovary	ovary
15	chr8:8168600-8174800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr8:8168600-8174800	Weak transcription	Fetal Stomach	stomach
17	chr8:8168800-8173800	Weak transcription	Fetal Muscle Leg	muscle
18	chr8:8168800-8174200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr8:8168800-8174200	Enhancers	Hela-S3	cervix
20	chr8:8168800-8174400	Weak transcription	HSMM	muscle
21	chr8:8168800-8175600	Weak transcription	Right Ventricle	heart
22	chr8:8168800-8181400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr8:8168800-8187400	Weak transcription	Small Intestine	intestine
24	chr8:8169000-8174600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr8:8169000-8181200	Weak transcription	Brain Angular Gyrus	brain
26	chr8:8169000-8181400	Weak transcription	Colon Smooth Muscle	Colon
27	chr8:8169200-8174000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr8:8169200-8174000	Weak transcription	Osteobl	bone
29	chr8:8169200-8174600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr8:8169600-8174600	Weak transcription	NHLF	lung
31	chr8:8169800-8173800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr8:8169800-8174000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:8170000-8174000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr8:8170000-8174600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:8170000-8174600	Weak transcription	Placenta	Placenta
36	chr8:8170000-8174600	Weak transcription	Lung	lung
37	chr8:8170200-8173800	Weak transcription	Primary B cells from cord blood	blood
38	chr8:8170200-8173800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr8:8170400-8174600	Weak transcription	Fetal Intestine Small	intestine
40	chr8:8170600-8173800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:8170600-8174200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr8:8170600-8174600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr8:8170600-8174600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr8:8170600-8175600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr8:8170600-8184000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr8:8170800-8173800	Weak transcription	Primary T cells from cord blood	blood
47	chr8:8170800-8174000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr8:8171000-8173800	Weak transcription	HMEC	breast
49	chr8:8171000-8173800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr8:8171000-8174000	Weak transcription	Primary monocytes fromperipheralblood	blood

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