Variant report

Variant	rs934847
Chromosome Location	chr12:104185693-104185694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104185307-104185851	K562	blood:	n/a	n/a
2	POLR2A	chr12:104185012-104185809	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104183971..104186585-chr12:104195377..104197351,2	MCF-7	breast:
2	chr12:104181732..104183493-chr12:104185105..104187662,2	K562	blood:
3	chr12:104183709..104186598-chr12:104189875..104192288,3	K562	blood:
4	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:

No data

Variant related genes	Relation type
NT5DC3	TF binding region
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10861094	0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861095	0.82[AMR][1000 genomes]
rs10861096	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs10861097	0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs10861099	0.80[GIH][hapmap];0.83[TSI][hapmap]
rs10861102	0.98[AFR][1000 genomes]
rs10861103	0.98[AFR][1000 genomes]
rs10861105	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11111752	0.80[EUR][1000 genomes]
rs11111754	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11111755	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11111758	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11111759	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11111762	0.81[AMR][1000 genomes]
rs11111767	0.85[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11111771	0.85[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111772	0.96[AFR][1000 genomes]
rs11111773	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs11111775	0.98[AFR][1000 genomes]
rs11111776	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111778	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11111779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111781	0.93[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs11111782	0.93[ASW][hapmap];0.80[GIH][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs11111783	0.93[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs11111786	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111787	0.96[AFR][1000 genomes]
rs11111788	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11111789	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11111792	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11111795	0.90[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs12229276	0.90[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs12424737	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12830701	0.84[AMR][1000 genomes]
rs1370777	0.87[ASW][hapmap];0.80[GIH][hapmap];0.91[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1370778	0.98[AFR][1000 genomes]
rs1370779	0.98[AFR][1000 genomes]
rs1565773	0.80[EUR][1000 genomes]
rs1866292	0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1866293	0.98[AFR][1000 genomes]
rs1866294	0.93[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs1866295	0.93[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1866296	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs1968513	0.98[AFR][1000 genomes]
rs1976256	0.81[EUR][1000 genomes]
rs2292682	0.80[EUR][1000 genomes]
rs2888792	0.98[AFR][1000 genomes]
rs34307072	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35945096	0.81[AMR][1000 genomes]
rs3751204	0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs3812803	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs3812805	0.83[MEX][hapmap]
rs4964786	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4964794	0.93[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4964805	0.93[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4964806	0.93[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4964812	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964813	0.98[AFR][1000 genomes]
rs4964814	0.93[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs4964819	0.98[AFR][1000 genomes]
rs4964820	0.93[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs4964823	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964827	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964830	0.83[MEX][hapmap]
rs4981032	0.82[AMR][1000 genomes]
rs4981036	0.82[AMR][1000 genomes]
rs5001722	0.95[AFR][1000 genomes]
rs58421738	0.98[AFR][1000 genomes]
rs7134701	0.93[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7312606	0.98[AFR][1000 genomes]
rs7312825	0.98[AFR][1000 genomes]
rs73192049	0.93[AFR][1000 genomes]
rs73192053	0.87[AFR][1000 genomes]
rs751448	0.83[MEX][hapmap]
rs869993	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9132	0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs934843	0.93[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs934845	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs934846	0.98[AFR][1000 genomes]
rs9706225	0.98[AFR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs934847	RP11-341G23.4	cis	Esophagus Muscularis	GTEx
rs934847	SKA3	trans	parietal	SCAN
rs934847	C12orf45	cis	cerebellum	SCAN
rs934847	RP11-341G23.4	cis	Thyroid	GTEx
rs934847	NT5DC3	cis	parietal	SCAN
rs934847	RP11-341G23.4	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
3	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
6	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
7	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:104171400-104188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:104171600-104187400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
14	chr12:104171800-104187600	Weak transcription	Fetal Brain Female	brain
15	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:104172400-104186400	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:104174200-104186200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:104175000-104187000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:104175200-104190000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:104178200-104186400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:104178200-104187600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:104178400-104188400	Weak transcription	Brain Anterior Caudate	brain
27	chr12:104178600-104193400	Weak transcription	Left Ventricle	heart
28	chr12:104178800-104186400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:104178800-104186600	Weak transcription	Colonic Mucosa	Colon
30	chr12:104178800-104194000	Weak transcription	Brain Angular Gyrus	brain
31	chr12:104178800-104194200	Weak transcription	Esophagus	oesophagus
32	chr12:104179000-104185800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:104179000-104186000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:104179000-104186400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:104179000-104186400	Weak transcription	Primary B cells from cord blood	blood
36	chr12:104179000-104187000	Weak transcription	Pancreas	Pancrea
37	chr12:104179000-104187000	Weak transcription	Psoas Muscle	Psoas
38	chr12:104179000-104188000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:104179000-104188400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:104179000-104188600	Weak transcription	Lung	lung
41	chr12:104179000-104190600	Weak transcription	Gastric	stomach
42	chr12:104179000-104193200	Weak transcription	Spleen	Spleen
43	chr12:104179000-104193600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:104179200-104186400	Weak transcription	HSMMtube	muscle
45	chr12:104179200-104188200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:104179400-104185800	Weak transcription	Adipose Nuclei	Adipose
47	chr12:104179400-104186400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr12:104179400-104188400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:104179400-104191400	Weak transcription	Hela-S3	cervix
50	chr12:104179400-104193800	Weak transcription	Fetal Kidney	kidney

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