Variant report

Variant	rs934843
Chromosome Location	chr12:104185132-104185133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104185012-104185809	K562	blood:	n/a	n/a
2	POLR2A	chr12:104184840-104185303	K562	blood:	n/a	n/a
3	POLR2A	chr12:104184874-104185521	K562	blood:	n/a	n/a
4	CTCF	chr12:104185100-104185250	BE2_C	brain:	n/a	n/a
5	NFIC	chr12:104185047-104185601	ECC-1	luminal epithelium:	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: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10735389	0.81[CHD][hapmap]
rs10778285	1.00[ASN][1000 genomes]
rs10861092	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10861093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10861096	0.86[ASW][hapmap]
rs10861097	0.86[ASW][hapmap]
rs10861098	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861099	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861102	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861105	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs11111751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111761	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111764	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111766	1.00[ASN][1000 genomes]
rs11111767	0.87[TSI][hapmap]
rs11111771	0.87[TSI][hapmap]
rs11111772	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111773	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111776	0.97[AFR][1000 genomes]
rs11111779	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs11111781	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111782	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111783	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111786	0.96[AFR][1000 genomes]
rs11111787	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111788	0.98[AFR][1000 genomes]
rs11111789	0.95[AFR][1000 genomes]
rs11111792	0.89[AFR][1000 genomes]
rs11111795	0.82[GIH][hapmap]
rs12229276	0.82[GIH][hapmap]
rs12424737	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12425205	0.84[CHD][hapmap]
rs1370777	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1370779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866292	0.87[TSI][hapmap]
rs1866293	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866294	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866295	1.00[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs1866296	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1968513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2888792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751204	0.86[ASW][hapmap]
rs3751205	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3812804	0.85[CHD][hapmap]
rs4964794	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4964805	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4964806	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4964812	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs4964813	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964814	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964819	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964820	1.00[ASW][hapmap];0.96[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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981034	0.81[CHD][hapmap]
rs4981035	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5001722	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58421738	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61602054	0.97[ASN][1000 genomes]
rs6539101	0.85[CHD][hapmap]
rs7134701	0.86[ASW][hapmap];0.82[GIH][hapmap]
rs7136682	0.91[ASN][1000 genomes]
rs7296900	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312606	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312825	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73192049	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73192053	0.85[AFR][1000 genomes]
rs7970553	0.85[CHD][hapmap]
rs7973081	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9084	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9132	0.86[ASW][hapmap]
rs9142	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs934845	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934846	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs934847	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]
rs954921	0.86[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap]
rs9706225	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs934843	TU12B1-TY	cis	multi-tissue	Pritchard
rs934843	C12orf45	cis	cerebellum	SCAN
rs934843	SKA3	trans	parietal	SCAN
rs934843	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	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
4	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
7	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
8	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
10	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:104171400-104188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:104171600-104187400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
16	chr12:104171800-104187600	Weak transcription	Fetal Brain Female	brain
17	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:104172400-104186400	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:104174200-104185200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:104174200-104186200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:104175000-104187000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:104175200-104190000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:104178200-104186400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:104178200-104187600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:104178400-104185400	Weak transcription	Right Ventricle	heart
30	chr12:104178400-104185600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:104178400-104188400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:104178600-104193400	Weak transcription	Left Ventricle	heart
33	chr12:104178800-104185400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:104178800-104185400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:104178800-104186400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:104178800-104186600	Weak transcription	Colonic Mucosa	Colon
37	chr12:104178800-104194000	Weak transcription	Brain Angular Gyrus	brain
38	chr12:104178800-104194200	Weak transcription	Esophagus	oesophagus
39	chr12:104179000-104185200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:104179000-104185200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:104179000-104185400	Weak transcription	Ovary	ovary
42	chr12:104179000-104185600	Weak transcription	GM12878-XiMat	blood
43	chr12:104179000-104185800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:104179000-104186000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:104179000-104186400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr12:104179000-104186400	Weak transcription	Primary B cells from cord blood	blood
47	chr12:104179000-104187000	Weak transcription	Pancreas	Pancrea
48	chr12:104179000-104187000	Weak transcription	Psoas Muscle	Psoas
49	chr12:104179000-104188000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:104179000-104188400	Weak transcription	Brain Inferior Temporal Lobe	brain

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