Variant report

Variant	rs12830678
Chromosome Location	chr12:29503676-29503677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr12:29502783-29503724	ECC-1	luminal epithelium:	n/a	n/a
2	GATA3	chr12:29502857-29503684	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29503193..29506083-chr12:30783016..30785826,2	MCF-7	breast:

Variant related genes	Relation type
ERGIC2	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10492377	0.84[CEU][hapmap]
rs10492383	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11608616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11609540	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11610197	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11610910	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11611420	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611687	0.85[EUR][1000 genomes]
rs11612172	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11613628	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11614129	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11614901	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11615636	0.85[EUR][1000 genomes]
rs12809493	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12810064	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810315	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12811201	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12811723	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12813520	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12813731	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12813789	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12813996	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12814180	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814930	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12815222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816511	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs12817163	0.84[EUR][1000 genomes]
rs12817578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817825	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817985	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12819896	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12821498	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12821559	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12821708	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823372	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823422	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12823485	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823903	0.85[EUR][1000 genomes]
rs12824407	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12829666	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830274	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12830493	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830906	0.85[EUR][1000 genomes]
rs12831730	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12832038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12832263	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1988943	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2350312	0.85[EUR][1000 genomes]
rs2882377	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35618989	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35636563	0.85[EUR][1000 genomes]
rs36126531	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3764952	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4369447	1.00[CEU][hapmap]
rs67280216	0.85[EUR][1000 genomes]
rs7134744	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7295387	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308372	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7314594	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7961336	0.85[EUR][1000 genomes]
rs7964254	0.85[EUR][1000 genomes]
rs7979654	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1796867	chr12:29501941-29524159	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12830678	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs12830678	RP11-996F15.2	cis	Artery Tibial	GTEx
rs12830678	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs12830678	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12830678	RP11-996F15.2	cis	lung	GTEx
rs12830678	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs12830678	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
3	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
5	chr12:29473800-29522600	Weak transcription	NHEK	skin
6	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
7	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
9	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:29477000-29517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:29483400-29518000	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
15	chr12:29485600-29533400	Weak transcription	Gastric	stomach
16	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
17	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:29488600-29503800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:29488800-29532000	Weak transcription	NHLF	lung
20	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:29489800-29510000	Weak transcription	Brain Germinal Matrix	brain
22	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
24	chr12:29490200-29506000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:29491000-29511400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:29491400-29506400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:29492400-29511800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:29492400-29518000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:29492800-29511800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:29492800-29519000	Weak transcription	HepG2	liver
32	chr12:29493200-29504800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:29494400-29517800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
36	chr12:29494600-29509000	Weak transcription	Lung	lung
37	chr12:29494600-29511800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
39	chr12:29496400-29509200	Weak transcription	Left Ventricle	heart
40	chr12:29496400-29518000	Weak transcription	Brain Anterior Caudate	brain
41	chr12:29496400-29518000	Weak transcription	Thymus	Thymus
42	chr12:29496400-29532200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr12:29496600-29517800	Weak transcription	NH-A	brain
44	chr12:29496800-29508600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:29496800-29519000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr12:29497000-29509000	Weak transcription	HMEC	breast
47	chr12:29497400-29532400	Weak transcription	Fetal Heart	heart
48	chr12:29497600-29518200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:29498000-29504400	Weak transcription	Brain Angular Gyrus	brain
50	chr12:29498000-29515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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