Variant report

Variant	rs3812805
Chromosome Location	chr12:104170872-104170873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104168307..104171120-chr12:104193442..104196343,2	K562	blood:
2	chr12:104166229..104169114-chr12:104169303..104172896,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10861094	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861096	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861104	0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs11111750	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111752	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111754	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111755	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111757	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111758	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11111759	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11111762	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111763	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111765	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111767	0.92[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111771	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11111776	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11111778	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111791	0.80[ASN][1000 genomes]
rs11111796	0.82[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs11610714	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs12228207	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs12229292	0.82[CHB][hapmap]
rs1565773	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs15918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866292	0.92[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1976256	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292682	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3751204	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964289	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs4964298	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964780	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4964823	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964827	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4981032	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4981036	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs751448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs869993	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs934847	0.83[MEX][hapmap]
rs954920	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954921	0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv899491	chr12:104151560-104175575	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3812805	RP11-341G23.4	cis	Artery Tibial	GTEx
rs3812805	NT5DC3	cis	parietal	SCAN
rs3812805	RP11-341G23.4	cis	Adipose Subcutaneous	GTEx
rs3812805	RP11-341G23.4	cis	Artery Aorta	GTEx
rs3812805	RP11-341G23.4	cis	Thyroid	GTEx
rs3812805	RP11-341G23.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104152600-104171200	Weak transcription	Esophagus	oesophagus
2	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:104155000-104171000	Weak transcription	Osteobl	bone
5	chr12:104155000-104178000	Weak transcription	Colonic Mucosa	Colon
6	chr12:104155200-104173400	Weak transcription	NHDF-Ad	bronchial
7	chr12:104157400-104172400	Weak transcription	GM12878-XiMat	blood
8	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
9	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:104163000-104178400	Strong transcription	NHEK	skin
11	chr12:104163200-104175200	Weak transcription	Psoas Muscle	Psoas
12	chr12:104163600-104174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:104163600-104185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:104163800-104171000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:104164400-104171600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:104165800-104173800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
19	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
20	chr12:104167000-104173400	Weak transcription	Right Ventricle	heart
21	chr12:104167000-104174400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:104167200-104173600	Weak transcription	Fetal Heart	heart
23	chr12:104167200-104176000	Weak transcription	Small Intestine	intestine
24	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:104167400-104171000	Weak transcription	Brain Substantia Nigra	brain
26	chr12:104167800-104173800	Strong transcription	A549	lung
27	chr12:104168000-104176800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:104168000-104178800	Weak transcription	Hela-S3	cervix
29	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
30	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:104168200-104173600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:104168400-104173600	Strong transcription	HMEC	breast
33	chr12:104168600-104180800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr12:104168800-104171600	Strong transcription	NH-A	brain
35	chr12:104168800-104171800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:104168800-104171800	Strong transcription	Fetal Muscle Leg	muscle
37	chr12:104168800-104172000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:104168800-104172600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:104168800-104172800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:104168800-104173200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:104168800-104174000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:104168800-104174000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:104168800-104174200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr12:104168800-104175400	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:104169000-104171000	Weak transcription	Pancreas	Pancrea
46	chr12:104169000-104174200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:104169000-104175000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:104169000-104176800	Strong transcription	Liver	Liver
49	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:104169200-104172200	Strong transcription	HSMM	muscle

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