Variant report

Variant	rs6488100
Chromosome Location	chr12:9820619-9820620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9819935-9822633	GM12891	blood:	n/a	n/a
2	NFIC	chr12:9820569-9821216	SK-N-SH	brain:	n/a	n/a
3	STAT3	chr12:9820413-9820670	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:9820403-9820691	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr12:9820335-9821010	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr12:9820406-9821007	MCF10A-Er-Src	breast:	n/a	n/a
7	CHD1	chr12:9819935-9820676	GM12878	blood:	n/a	n/a
8	NFIC	chr12:9819870-9820734	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9815292..9817127-chr12:9818651..9820715,3	MCF-7	breast:

Variant related genes	Relation type
CLEC2D	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10732553	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771987	0.86[YRI][hapmap]
rs10771997	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10771999	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10844372	1.00[CHB][hapmap]
rs11052241	1.00[CHB][hapmap]
rs1108452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560007	0.86[YRI][hapmap]
rs16914640	1.00[CHB][hapmap]
rs17732859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176798	1.00[CHB][hapmap]
rs4439599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131784	0.86[YRI][hapmap]
rs7306991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316769	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237255	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
3	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
4	chr12:9806200-9821600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr12:9807000-9826000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:9812800-9825800	Weak transcription	Right Ventricle	heart
8	chr12:9813000-9825800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:9813000-9826200	Weak transcription	Brain Anterior Caudate	brain
10	chr12:9813000-9826200	Weak transcription	Gastric	stomach
11	chr12:9813800-9826000	Weak transcription	NHDF-Ad	bronchial
12	chr12:9815000-9820800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:9815000-9822400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:9815000-9826000	Weak transcription	Lung	lung
15	chr12:9815000-9826000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:9815000-9826200	Weak transcription	Colonic Mucosa	Colon
17	chr12:9815000-9826200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:9815000-9826400	Weak transcription	Fetal Intestine Small	intestine
19	chr12:9815200-9824000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:9815200-9825000	Weak transcription	K562	blood
21	chr12:9815200-9825800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:9815200-9825800	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:9815200-9826200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:9815200-9828400	Weak transcription	Liver	Liver
25	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
26	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
27	chr12:9815400-9825000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:9815400-9825600	Weak transcription	HepG2	liver
29	chr12:9815600-9825200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:9815600-9825600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:9815600-9825800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:9815600-9826000	Weak transcription	Spleen	Spleen
33	chr12:9815600-9833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:9815800-9825600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:9816200-9832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:9817000-9826000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:9817200-9824800	Weak transcription	Dnd41	blood
39	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
40	chr12:9817600-9825400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:9817600-9826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:9818000-9825800	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:9818000-9825800	Weak transcription	Placenta	Placenta
44	chr12:9818000-9826000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:9818000-9826000	Weak transcription	Fetal Stomach	stomach
46	chr12:9818000-9826000	Weak transcription	Left Ventricle	heart
47	chr12:9818000-9826200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:9818000-9839800	Weak transcription	Ovary	ovary
50	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine

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