Variant report

Variant	rs3935416
Chromosome Location	chr12:104206955-104206956
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104206123..104208804-chr12:104221926..104227695,4	K562	blood:
2	chr12:104206137..104208857-chr12:104227836..104229349,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10861104	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10861105	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10861109	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111786	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11111788	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11111789	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11111791	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11111792	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111793	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111795	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111796	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12228207	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12229276	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830701	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866295	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34307072	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35371470	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35746861	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35945096	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36034617	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812803	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964289	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4964623	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964780	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4964786	1.00[ASN][1000 genomes]
rs4964794	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964805	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964806	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964812	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67825151	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7134701	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3935416	RP11-341G23.4	cis	Artery Tibial	GTEx
rs3935416	RP11-341G23.4	cis	Thyroid	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
5	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:104194400-104207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:104194600-104207000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:104194600-104214600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:104194600-104214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:104194800-104207200	Weak transcription	Adipose Nuclei	Adipose
13	chr12:104194800-104215200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:104195000-104207800	Weak transcription	Fetal Lung	lung
15	chr12:104195000-104208600	Weak transcription	Left Ventricle	heart
16	chr12:104195000-104213800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:104195800-104208400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:104196400-104213600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:104196400-104214800	Weak transcription	Brain Substantia Nigra	brain
20	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
21	chr12:104196600-104207800	Weak transcription	HSMMtube	muscle
22	chr12:104196600-104212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:104196600-104213000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:104199200-104211000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:104199200-104211800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:104199600-104214600	Weak transcription	Esophagus	oesophagus
27	chr12:104200000-104214600	Weak transcription	Ovary	ovary
28	chr12:104200200-104207000	Weak transcription	Liver	Liver
29	chr12:104200200-104216200	Weak transcription	NHDF-Ad	bronchial
30	chr12:104200400-104210000	Weak transcription	Hela-S3	cervix
31	chr12:104200800-104207200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:104201000-104214600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:104201200-104207800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:104201200-104207800	Weak transcription	Placenta	Placenta
35	chr12:104201200-104207800	Strong transcription	A549	lung
36	chr12:104201400-104207800	Weak transcription	Lung	lung
37	chr12:104201400-104209000	Weak transcription	HUVEC	blood vessel
38	chr12:104201400-104214800	Weak transcription	NHLF	lung
39	chr12:104201600-104212600	Weak transcription	Psoas Muscle	Psoas
40	chr12:104201800-104208600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:104201800-104208800	Strong transcription	HMEC	breast
42	chr12:104202000-104207200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:104202000-104208800	Strong transcription	Primary B cells from cord blood	blood
44	chr12:104202200-104207000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:104202200-104207800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:104202200-104207800	Weak transcription	Spleen	Spleen
47	chr12:104202200-104209400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:104202200-104218200	Weak transcription	Gastric	stomach
49	chr12:104202400-104214800	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:104202600-104207400	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links