Variant report

Variant	rs7978051
Chromosome Location	chr12:104748365-104748366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104744585..104747269-chr12:104747658..104751523,4	K562	blood:
2	chr12:104741157..104743951-chr12:104747140..104749533,2	K562	blood:
3	chr12:104744585..104746510-chr12:104748282..104749996,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10778321	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10861185	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs10861187	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.92[ASN][1000 genomes]
rs10861190	0.84[ASN][1000 genomes]
rs10861193	0.92[ASN][1000 genomes]
rs10861195	0.92[ASN][1000 genomes]
rs10861196	0.92[ASN][1000 genomes]
rs10861197	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10861198	0.92[ASN][1000 genomes]
rs10861199	0.92[ASN][1000 genomes]
rs10861205	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861206	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861208	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861209	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861210	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861211	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11111979	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs11111980	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs11111981	0.92[ASN][1000 genomes]
rs11111984	0.92[ASN][1000 genomes]
rs11111987	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs11111995	0.92[ASN][1000 genomes]
rs11111996	0.92[ASN][1000 genomes]
rs11112006	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112007	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11609469	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811618	0.91[ASN][1000 genomes]
rs17202060	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs17202520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28672744	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4075411	0.92[ASN][1000 genomes]
rs4436618	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4595619	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4601859	0.92[ASN][1000 genomes]
rs4964782	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs4964783	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4964785	0.91[ASN][1000 genomes]
rs4964788	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5018287	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7132675	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7294778	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs7298739	0.92[ASN][1000 genomes]
rs7488680	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs7953266	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7977410	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7977553	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7978051	C12orf42	cis	cerebellum	SCAN
rs7978051	TDG	cis	parietal	SCAN
rs7978051	EID3	cis	normal skin	skin_eQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104703000-104749200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:104709800-104749200	Strong transcription	HUVEC	blood vessel
3	chr12:104721800-104760000	Weak transcription	Stomach Mucosa	stomach
4	chr12:104725000-104749400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:104727200-104748600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:104727400-104748600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:104727400-104749000	Strong transcription	HMEC	breast
8	chr12:104728800-104755000	Weak transcription	Fetal Heart	heart
9	chr12:104734000-104750400	Weak transcription	Fetal Brain Male	brain
10	chr12:104735200-104749000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:104738800-104748600	Strong transcription	NH-A	brain
12	chr12:104739400-104749600	Strong transcription	HSMM	muscle
13	chr12:104739600-104749000	Strong transcription	Thymus	Thymus
14	chr12:104740200-104749000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:104740200-104749200	Strong transcription	HSMMtube	muscle
16	chr12:104741000-104749200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:104741000-104749200	Strong transcription	NHLF	lung
18	chr12:104741200-104749000	Strong transcription	Primary T cells from cord blood	blood
19	chr12:104741200-104749200	Strong transcription	Left Ventricle	heart
20	chr12:104741600-104749000	Strong transcription	Fetal Muscle Leg	muscle
21	chr12:104741800-104750000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:104742800-104750000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:104742800-104750400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:104743000-104749000	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:104743600-104751200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:104744000-104748400	Weak transcription	Brain Germinal Matrix	brain
27	chr12:104744800-104749200	Weak transcription	Colonic Mucosa	Colon
28	chr12:104744800-104752000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:104745000-104749600	Weak transcription	Right Atrium	heart
30	chr12:104745000-104749800	Weak transcription	Fetal Kidney	kidney
31	chr12:104745000-104750400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:104745000-104750800	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:104745000-104752200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:104745000-104761400	Weak transcription	Psoas Muscle	Psoas
35	chr12:104745200-104748600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:104745200-104749200	Weak transcription	Fetal Intestine Large	intestine
37	chr12:104745200-104750400	Weak transcription	Esophagus	oesophagus
38	chr12:104745200-104750800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:104745400-104750600	Weak transcription	Brain Substantia Nigra	brain
40	chr12:104745400-104754000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:104745600-104750000	Weak transcription	Fetal Brain Female	brain
42	chr12:104745800-104754000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:104746000-104748600	Weak transcription	Fetal Lung	lung
44	chr12:104746000-104749200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:104746000-104750000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:104746000-104751000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:104746000-104756800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr12:104746200-104748400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:104746200-104748400	Weak transcription	Ovary	ovary
50	chr12:104746200-104748600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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