Variant report

Variant	rs869993
Chromosome Location	chr12:104175138-104175139
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104166261..104169463-chr12:104174698..104177836,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10861094	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10861095	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861096	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861097	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861098	0.84[AFR][1000 genomes]
rs10861099	0.84[AFR][1000 genomes]
rs10861104	0.82[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11111750	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111752	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111754	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11111755	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11111757	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111758	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11111759	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111762	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11111763	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11111765	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11111767	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11111771	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111776	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11111778	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111779	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111793	0.81[ASN][1000 genomes]
rs11111796	0.89[JPT][hapmap]
rs11610714	0.84[JPT][hapmap]
rs12228207	0.89[JPT][hapmap]
rs12229292	0.81[JPT][hapmap]
rs1565773	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs15918	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1866292	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976256	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292682	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3751204	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812805	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]
rs4964289	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs4964298	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964780	0.90[JPT][hapmap]
rs4964823	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964827	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964830	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]
rs4981032	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4981036	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67825151	0.80[ASN][1000 genomes]
rs751448	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9132	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs934847	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs954920	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs954921	0.92[YRI][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs869993	RP11-341G23.4	cis	Esophagus Muscularis	GTEx
rs869993	RP11-341G23.4	cis	Artery Tibial	GTEx
rs869993	RP11-341G23.4	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104155000-104178000	Weak transcription	Colonic Mucosa	Colon
4	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
5	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:104163000-104178400	Strong transcription	NHEK	skin
7	chr12:104163200-104175200	Weak transcription	Psoas Muscle	Psoas
8	chr12:104163600-104185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
11	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
12	chr12:104167200-104176000	Weak transcription	Small Intestine	intestine
13	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:104168000-104176800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:104168000-104178800	Weak transcription	Hela-S3	cervix
16	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
17	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:104168600-104180800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr12:104168800-104175400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:104169000-104176800	Strong transcription	Liver	Liver
21	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:104169200-104180200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:104169600-104184800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:104170400-104179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:104170400-104180400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:104170600-104175200	Strong transcription	Adipose Nuclei	Adipose
27	chr12:104170600-104177200	Strong transcription	Fetal Intestine Large	intestine
28	chr12:104170600-104179400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr12:104170800-104175800	Strong transcription	HepG2	liver
30	chr12:104170800-104176600	Strong transcription	Fetal Intestine Small	intestine
31	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:104171400-104177800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:104171400-104188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:104171600-104176400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:104171600-104178200	Weak transcription	Primary B cells from cord blood	blood
36	chr12:104171600-104187400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
38	chr12:104171800-104177000	Weak transcription	Brain Angular Gyrus	brain
39	chr12:104171800-104177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:104171800-104177600	Weak transcription	Brain Anterior Caudate	brain
41	chr12:104171800-104178200	Weak transcription	Pancreas	Pancrea
42	chr12:104171800-104187600	Weak transcription	Fetal Brain Female	brain
43	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:104172000-104177600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:104172000-104178200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:104172400-104176800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:104172400-104186400	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:104173000-104179400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:104173400-104175400	Strong transcription	Gastric	stomach

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