Variant report

Variant	rs7554012
Chromosome Location	chr1:62190408-62190409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:62172803..62176394-chr1:62188013..62191041,5	K562	blood:
2	chr1:62148615..62150124-chr1:62189264..62192017,2	MCF-7	breast:
3	chr1:62190320..62192154-chr1:62900473..62901978,2	MCF-7	breast:
4	chr1:62173473..62177807-chr1:62188633..62191997,6	K562	blood:
5	chr1:62189472..62191047-chr17:57915303..57918129,2	MCF-7	breast:
6	chr1:62149064..62151297-chr1:62189288..62192078,2	K562	blood:
7	chr1:62188914..62195188-chr1:62202056..62212232,19	MCF-7	breast:
8	chr1:62187463..62192137-chr1:62206143..62210486,9	MCF-7	breast:
9	chr1:62190311..62190822-chr11:62572833..62573349,2	HCT-116	colon:

No data

Variant related genes	Relation type
ENSG00000271200	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000162604	Chromatin interaction
ENSG00000162607	Chromatin interaction
ENSG00000132849	Chromatin interaction
ENSG00000162231	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493311	0.89[ASW][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11539585	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11578760	0.81[AFR][1000 genomes]
rs11802679	0.89[ASW][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11805607	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375232	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1353424	1.00[EUR][1000 genomes]
rs1390450	0.82[AFR][1000 genomes]
rs17122675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17122684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17122726	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17122742	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1890262	1.00[EUR][1000 genomes]
rs2051137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57862885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57901641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61285999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6678289	0.89[ASW][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs6698090	1.00[EUR][1000 genomes]
rs72925623	1.00[EUR][1000 genomes]
rs72925628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925658	1.00[AMR][1000 genomes]
rs72925685	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925687	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72927617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72927635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7544197	1.00[EUR][1000 genomes]
rs7551993	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7554012	TM2D1	cis	multi-tissue	Pritchard
rs7554012	BBP	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62189000-62191400	Active TSS	NHLF	lung
2	chr1:62189200-62191600	Active TSS	K562	blood
3	chr1:62189400-62190600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr1:62189400-62191600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:62189400-62191600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:62189400-62191600	Active TSS	Fetal Lung	lung
7	chr1:62189400-62191800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:62189400-62191800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:62189400-62191800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:62189600-62190600	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr1:62189600-62191000	Active TSS	Muscle Satellite Cultured Cells	--
12	chr1:62189600-62191200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:62189600-62191400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:62189600-62191400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:62189600-62191400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:62189600-62191400	Active TSS	Colonic Mucosa	Colon
17	chr1:62189600-62191400	Active TSS	Left Ventricle	heart
18	chr1:62189600-62191400	Active TSS	Psoas Muscle	Psoas
19	chr1:62189600-62191400	Active TSS	Right Ventricle	heart
20	chr1:62189600-62191600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:62189600-62191600	Active TSS	Brain Angular Gyrus	brain
22	chr1:62189600-62191600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:62189600-62191600	Active TSS	Right Atrium	heart
24	chr1:62189600-62191600	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:62189600-62191600	Active TSS	A549	lung
26	chr1:62189600-62191600	Active TSS	NHDF-Ad	bronchial
27	chr1:62189800-62190600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr1:62189800-62190600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:62189800-62191000	Active TSS	HSMM	muscle
30	chr1:62189800-62191200	Active TSS	HMEC	breast
31	chr1:62189800-62191400	Active TSS	H9 Cell Line	embryonic stem cell
32	chr1:62189800-62191400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr1:62189800-62191400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:62189800-62191400	Active TSS	Fetal Heart	heart
35	chr1:62189800-62191400	Active TSS	Osteobl	bone
36	chr1:62189800-62191600	Active TSS	H1 Cell Line	embryonic stem cell
37	chr1:62189800-62191600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:62189800-62191600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:62189800-62191600	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr1:62189800-62191600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:62189800-62191600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:62189800-62191600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr1:62189800-62191800	Active TSS	GM12878-XiMat	blood
44	chr1:62190000-62190600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr1:62190000-62190600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr1:62190000-62191000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:62190000-62191000	Active TSS	Dnd41	blood
48	chr1:62190000-62191000	Active TSS	HUVEC	blood vessel
49	chr1:62190000-62191200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:62190000-62191200	Active TSS	Gastric	stomach

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