Variant report

Variant	rs7977104
Chromosome Location	chr12:51559511-51559512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51557800..51560550-chr12:51563372..51565178,2	K562	blood:
2	chr12:51557800..51560128-chr12:51563372..51565944,2	K562	blood:
3	chr12:51557818..51560220-chr12:51566523..51568651,2	K562	blood:

Variant related genes	Relation type
ENSG00000135457	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1048230	0.88[GIH][hapmap];0.80[TSI][hapmap]
rs1056897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169654	0.88[GIH][hapmap];0.80[TSI][hapmap]
rs11169726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169732	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169736	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169742	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169743	0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169752	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169754	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11738	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11833022	0.94[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs11834746	0.80[JPT][hapmap]
rs12809832	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12810455	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12810596	0.84[AMR][1000 genomes]
rs12810700	1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs12811508	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12811684	0.81[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs12813368	0.82[AMR][1000 genomes]
rs12814498	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12815367	0.96[ASN][1000 genomes]
rs12819225	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12819517	0.81[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12820559	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12820966	0.82[AMR][1000 genomes]
rs12823402	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12826153	0.81[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs12829630	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12833565	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17125137	0.85[GIH][hapmap]
rs17296192	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2285230	0.88[GIH][hapmap]
rs2301529	0.88[GIH][hapmap];0.80[TSI][hapmap]
rs34057357	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34481246	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34498074	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768967	0.94[GIH][hapmap];0.83[TSI][hapmap]
rs6580784	0.94[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs6580792	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580793	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67293043	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7954140	0.94[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs7955251	0.96[ASN][1000 genomes]
rs7958064	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7960381	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7964570	0.88[AMR][1000 genomes]
rs7976777	0.84[AMR][1000 genomes]
rs7978723	0.91[GIH][hapmap];0.84[MEX][hapmap]
rs970098	0.82[AMR][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	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	esv2762980	chr12:51527963-51561056	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7977104	TMPRSS12	cis	parietal	SCAN
rs7977104	COL2A1	cis	cerebellum	SCAN
rs7977104	CSRNP2	cis	cerebellum	SCAN
rs7977104	TFCP2	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51503200-51560200	Weak transcription	Right Ventricle	heart
2	chr12:51504800-51563400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:51513000-51565400	Weak transcription	Fetal Lung	lung
4	chr12:51519000-51561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:51519000-51565000	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:51519000-51565200	Weak transcription	Left Ventricle	heart
7	chr12:51519000-51565200	Weak transcription	Pancreas	Pancrea
8	chr12:51519000-51565800	Weak transcription	Esophagus	oesophagus
9	chr12:51519200-51559600	Weak transcription	Lung	lung
10	chr12:51519200-51563800	Weak transcription	Fetal Brain Female	brain
11	chr12:51519200-51565000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:51519400-51565200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:51521600-51565200	Weak transcription	HSMM	muscle
14	chr12:51527400-51565200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:51530600-51564200	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:51531200-51563400	Weak transcription	Hela-S3	cervix
17	chr12:51532000-51565000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:51532400-51564000	Weak transcription	Primary T cells from cord blood	blood
19	chr12:51532600-51562000	Weak transcription	Ovary	ovary
20	chr12:51532600-51562800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:51532600-51564800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:51532600-51565200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:51532800-51563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:51533000-51563200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:51533200-51561400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:51533200-51561400	Weak transcription	Placenta	Placenta
27	chr12:51533200-51564800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:51533400-51560200	Weak transcription	Dnd41	blood
29	chr12:51533600-51564800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:51533600-51565000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:51534600-51564200	Weak transcription	Fetal Intestine Large	intestine
32	chr12:51539600-51565000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:51539800-51561000	Weak transcription	Aorta	Aorta
34	chr12:51540000-51560200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:51540800-51564800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:51541000-51560200	Weak transcription	Primary B cells from cord blood	blood
37	chr12:51543200-51565200	Weak transcription	Psoas Muscle	Psoas
38	chr12:51545000-51564200	Weak transcription	Brain Germinal Matrix	brain
39	chr12:51545000-51565000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:51545000-51565000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:51550200-51563200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:51550400-51565400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:51550600-51560200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:51550800-51560200	Weak transcription	NHEK	skin
45	chr12:51550800-51564800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:51551400-51562400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:51552200-51563600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:51552400-51565000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:51553200-51565000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:51553800-51559800	Weak transcription	Spleen	Spleen

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