Variant report

Variant	rs17312971
Chromosome Location	chr1:62189541-62189542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr1:62173473..62177807-chr1:62188633..62191997,6	K562	blood:
4	chr1:62189472..62191047-chr17:57915303..57918129,2	MCF-7	breast:
5	chr1:62149064..62151297-chr1:62189288..62192078,2	K562	blood:
6	chr1:62188914..62195188-chr1:62202056..62212232,19	MCF-7	breast:
7	chr1:62187463..62192137-chr1:62206143..62210486,9	MCF-7	breast:

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

Extended variants
information (count: 5 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs35138123	0.86[ASN][1000 genomes]
rs61770086	0.86[ASN][1000 genomes]
rs61770105	0.87[AFR][1000 genomes];0.97[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17312971	TM2D1	cis	multi-tissue	Pritchard
rs17312971	TM2D1	cis	cerebellum	SCAN
rs17312971	TM2D1	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
2	chr1:62146200-62190200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:62158600-62189800	Weak transcription	Pancreas	Pancrea
4	chr1:62165000-62189800	Weak transcription	Aorta	Aorta
5	chr1:62165400-62189600	Weak transcription	Right Ventricle	heart
6	chr1:62165400-62189800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:62172000-62189800	Weak transcription	Gastric	stomach
8	chr1:62173200-62189600	Weak transcription	Colonic Mucosa	Colon
9	chr1:62174000-62189600	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:62174400-62189800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:62174400-62189800	Weak transcription	Esophagus	oesophagus
12	chr1:62174600-62190200	Weak transcription	Small Intestine	intestine
13	chr1:62174800-62189600	Weak transcription	Primary B cells from cord blood	blood
14	chr1:62174800-62189600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:62174800-62189600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:62174800-62189600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:62174800-62189600	Weak transcription	Left Ventricle	heart
18	chr1:62174800-62189600	Weak transcription	Osteobl	bone
19	chr1:62174800-62189800	Weak transcription	Lung	lung
20	chr1:62174800-62189800	Weak transcription	HSMMtube	muscle
21	chr1:62174800-62190000	Weak transcription	Ovary	ovary
22	chr1:62174800-62190400	Weak transcription	Spleen	Spleen
23	chr1:62175000-62189600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:62175000-62189800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:62175000-62189800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:62175200-62189600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:62175200-62189800	Weak transcription	Stomach Mucosa	stomach
28	chr1:62175200-62190000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:62175400-62189600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:62175400-62189600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:62175400-62189600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:62175400-62189800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:62175600-62189600	Weak transcription	HSMM	muscle
34	chr1:62176200-62189600	Weak transcription	Right Atrium	heart
35	chr1:62181200-62189600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:62182000-62189800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:62183800-62189600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:62184000-62190400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:62185000-62189600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:62186800-62189600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:62186800-62189600	Weak transcription	Fetal Intestine Large	intestine
42	chr1:62186800-62189800	Weak transcription	Placenta	Placenta
43	chr1:62187000-62189600	Weak transcription	Fetal Thymus	thymus
44	chr1:62187000-62189800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:62187200-62189600	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:62187200-62189800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:62187400-62189800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:62187800-62189600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:62187800-62189600	Weak transcription	Thymus	Thymus
50	chr1:62188000-62189600	Weak transcription	Fetal Stomach	stomach

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