Variant report

Variant	rs11112006
Chromosome Location	chr12:104749457-104749458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104749005..104751520-chr12:104753750..104756278,3	K562	blood:
2	chr12:104744585..104747269-chr12:104747658..104751523,4	K562	blood:
3	chr12:104741157..104743951-chr12:104747140..104749533,2	K562	blood:
4	chr12:104744585..104746510-chr12:104748282..104749996,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10778321	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10861185	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs10861187	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.92[ASN][1000 genomes]
rs10861190	0.84[ASN][1000 genomes]
rs10861193	0.92[ASN][1000 genomes]
rs10861195	0.92[ASN][1000 genomes]
rs10861196	0.92[ASN][1000 genomes]
rs10861197	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10861198	0.92[ASN][1000 genomes]
rs10861199	0.92[ASN][1000 genomes]
rs10861205	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861206	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861208	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861209	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861210	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861211	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11111979	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs11111980	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs11111981	0.92[ASN][1000 genomes]
rs11111984	0.92[ASN][1000 genomes]
rs11111987	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs11111995	0.92[ASN][1000 genomes]
rs11111996	0.92[ASN][1000 genomes]
rs11112007	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11609469	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811618	0.91[ASN][1000 genomes]
rs17202060	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs17202520	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28672744	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4075411	0.92[ASN][1000 genomes]
rs4436618	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4595619	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4601859	0.92[ASN][1000 genomes]
rs4964782	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs4964783	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4964785	0.91[ASN][1000 genomes]
rs4964788	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5018287	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7132675	0.89[ASN][1000 genomes]
rs7294778	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs7298739	0.92[ASN][1000 genomes]
rs7488680	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs7953266	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7977410	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7977553	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11112006	EID3	cis	normal skin	skin_eQTL
rs11112006	TDG	cis	parietal	SCAN
rs11112006	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104721800-104760000	Weak transcription	Stomach Mucosa	stomach
2	chr12:104728800-104755000	Weak transcription	Fetal Heart	heart
3	chr12:104734000-104750400	Weak transcription	Fetal Brain Male	brain
4	chr12:104739400-104749600	Strong transcription	HSMM	muscle
5	chr12:104741800-104750000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:104742800-104750000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:104742800-104750400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:104743600-104751200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:104744800-104752000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:104745000-104749600	Weak transcription	Right Atrium	heart
11	chr12:104745000-104749800	Weak transcription	Fetal Kidney	kidney
12	chr12:104745000-104750400	Weak transcription	Brain Anterior Caudate	brain
13	chr12:104745000-104750800	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:104745000-104752200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:104745000-104761400	Weak transcription	Psoas Muscle	Psoas
16	chr12:104745200-104750400	Weak transcription	Esophagus	oesophagus
17	chr12:104745200-104750800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:104745400-104750600	Weak transcription	Brain Substantia Nigra	brain
19	chr12:104745400-104754000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:104745600-104750000	Weak transcription	Fetal Brain Female	brain
21	chr12:104745800-104754000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:104746000-104750000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:104746000-104751000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:104746000-104756800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:104746200-104749600	Weak transcription	Fetal Intestine Small	intestine
26	chr12:104746200-104749600	Weak transcription	Gastric	stomach
27	chr12:104746200-104750000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:104746200-104750200	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:104746200-104750400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:104746200-104750400	Weak transcription	Pancreas	Pancrea
31	chr12:104746200-104750600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:104746200-104750800	Weak transcription	Right Ventricle	heart
33	chr12:104746200-104751000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:104746200-104751200	Weak transcription	Fetal Stomach	stomach
35	chr12:104746200-104751200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:104746200-104754600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:104746200-104754800	Weak transcription	Hela-S3	cervix
38	chr12:104746200-104761200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:104746200-104763000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:104746400-104750200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:104746400-104752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:104746600-104750400	Weak transcription	GM12878-XiMat	blood
43	chr12:104746600-104750600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:104747000-104749600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:104747200-104750000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:104747200-104750200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:104747200-104750400	Weak transcription	Fetal Thymus	thymus
48	chr12:104747200-104750800	Weak transcription	Adipose Nuclei	Adipose
49	chr12:104747400-104749600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:104747400-104750600	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links