Variant report

Variant	rs2072116
Chromosome Location	chr12:48132451-48132452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48128880..48137705-chr12:48169546..48175532,12	K562	blood:
2	chr12:48129185..48133424-chr12:48134380..48137725,4	MCF-7	breast:
3	chr12:48125574..48127133-chr12:48129980..48132497,2	MCF-7	breast:
4	chr12:48130227..48133339-chr12:48139533..48144417,5	K562	blood:
5	chr12:48109273..48110145-chr12:48132178..48132996,2	K562	blood:
6	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1233062	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2238145	0.92[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2240108	1.00[CHD][hapmap]
rs3829317	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs757282	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977774	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886431	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929270	0.94[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2072116	HIATL1	cis	Cerebellum	GTEx
rs2072116	WNT1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48114000-48134400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:48114200-48132600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:48115600-48133600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:48115600-48134200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:48115600-48135000	Weak transcription	Primary T cells from cord blood	blood
6	chr12:48116200-48134000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:48126800-48133400	Enhancers	Ovary	ovary
8	chr12:48127000-48134000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:48127600-48135800	Enhancers	Fetal Muscle Trunk	muscle
10	chr12:48128000-48132600	Enhancers	Brain Anterior Caudate	brain
11	chr12:48128200-48132600	Enhancers	Fetal Heart	heart
12	chr12:48128200-48132600	Enhancers	Left Ventricle	heart
13	chr12:48128200-48135600	Enhancers	Right Atrium	heart
14	chr12:48128400-48135000	Weak transcription	NHEK	skin
15	chr12:48128800-48132600	Enhancers	NHDF-Ad	bronchial
16	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:48129200-48134000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:48129200-48134600	Weak transcription	Fetal Brain Female	brain
19	chr12:48129200-48137600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:48129400-48134000	Weak transcription	Fetal Brain Male	brain
21	chr12:48129400-48134200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:48129400-48138600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:48129600-48133000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:48129800-48137600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
27	chr12:48130200-48134800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:48130400-48134600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:48130400-48137600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:48130600-48133600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:48130600-48138800	Weak transcription	Fetal Intestine Large	intestine
32	chr12:48130800-48132800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:48130800-48133600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr12:48130800-48134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:48131000-48132600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:48131000-48133600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:48131000-48134600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
39	chr12:48131200-48132800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:48131200-48133800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:48131200-48141600	Weak transcription	Fetal Kidney	kidney
42	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:48131400-48132800	Enhancers	Right Ventricle	heart
44	chr12:48131400-48133600	Enhancers	Brain Germinal Matrix	brain
45	chr12:48131400-48133600	Weak transcription	Esophagus	oesophagus
46	chr12:48131400-48133600	Weak transcription	Psoas Muscle	Psoas
47	chr12:48131400-48133600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:48131400-48134400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:48131400-48134800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:48131600-48133600	Weak transcription	Colonic Mucosa	Colon

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