Variant report

Variant	rs41689
Chromosome Location	chr7:120633276-120633277
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120446160..120448246-chr7:120632744..120634259,2	K562	blood:
2	chr7:120631360..120633454-chr7:120681264..120683155,2	K562	blood:
3	chr7:120631497..120633631-chr7:120731853..120734107,2	K562	blood:
4	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
5	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:
6	chr7:120631348..120633454-chr7:120680148..120684056,4	K562	blood:

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10258025	0.81[EUR][1000 genomes]
rs10464522	0.87[ASN][1000 genomes]
rs193727	0.84[EUR][1000 genomes]
rs2074577	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2215789	0.84[EUR][1000 genomes]
rs2244863	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244865	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2248890	0.84[ASN][1000 genomes]
rs2525712	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525713	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525719	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525729	0.81[ASN][1000 genomes]
rs2525730	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2525735	0.82[EUR][1000 genomes]
rs2525736	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525737	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525738	0.85[EUR][1000 genomes]
rs2525739	0.85[EUR][1000 genomes]
rs2525740	0.85[EUR][1000 genomes]
rs2525741	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721354	0.81[ASN][1000 genomes]
rs2721358	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2721359	0.85[EUR][1000 genomes]
rs2721361	0.85[EUR][1000 genomes]
rs2721363	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721365	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721367	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721372	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41688	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41690	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41691	0.84[EUR][1000 genomes]
rs41692	0.84[EUR][1000 genomes]
rs41693	0.84[EUR][1000 genomes]
rs41694	0.84[EUR][1000 genomes]
rs41695	0.84[EUR][1000 genomes]
rs41697	0.84[EUR][1000 genomes]
rs41703	0.81[EUR][1000 genomes]
rs41704	0.81[EUR][1000 genomes]
rs6971619	0.86[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	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41689	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120627600-120633800	Active TSS	Stomach Smooth Muscle	stomach
2	chr7:120627800-120633600	Active TSS	Ovary	ovary
3	chr7:120627800-120633800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:120627800-120633800	Active TSS	Aorta	Aorta
5	chr7:120627800-120633800	Active TSS	Right Ventricle	heart
6	chr7:120628200-120633800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:120628800-120633600	Active TSS	NHLF	lung
8	chr7:120629400-120634000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:120629600-120635800	Weak transcription	Primary B cells from cord blood	blood
10	chr7:120629800-120633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:120630000-120633600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:120630000-120633600	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr7:120630000-120636400	Weak transcription	HMEC	breast
14	chr7:120630200-120633800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr7:120630200-120636200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:120630200-120636200	Weak transcription	Placenta	Placenta
17	chr7:120631200-120633800	Weak transcription	Left Ventricle	heart
18	chr7:120631200-120640400	Weak transcription	Brain Anterior Caudate	brain
19	chr7:120631400-120636200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:120632000-120633600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr7:120632000-120633600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:120632000-120633800	Weak transcription	Brain Hippocampus Middle	brain
23	chr7:120632000-120633800	Weak transcription	Psoas Muscle	Psoas
24	chr7:120632000-120634800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:120632000-120636400	Weak transcription	Hela-S3	cervix
26	chr7:120632200-120633600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:120632200-120636600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:120632400-120633800	Weak transcription	NH-A	brain
29	chr7:120632400-120634200	Transcr. at gene 5' and 3'	HSMM	muscle
30	chr7:120632400-120641400	Transcr. at gene 5' and 3'	K562	blood
31	chr7:120632600-120633400	Weak transcription	Fetal Stomach	stomach
32	chr7:120632600-120633800	Weak transcription	Fetal Muscle Leg	muscle
33	chr7:120632600-120634000	Enhancers	Colon Smooth Muscle	Colon
34	chr7:120632600-120634200	Enhancers	Fetal Lung	lung
35	chr7:120632600-120634600	Weak transcription	Fetal Heart	heart
36	chr7:120632600-120635000	Enhancers	Rectal Smooth Muscle	rectum
37	chr7:120632800-120633600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:120632800-120634400	Enhancers	Fetal Kidney	kidney
39	chr7:120633000-120633400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr7:120633000-120633400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:120633000-120633800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:120633000-120634000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:120633000-120634600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr7:120633000-120636600	Weak transcription	HSMMtube	muscle
45	chr7:120633000-120636800	Enhancers	Liver	Liver
46	chr7:120633000-120636800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr7:120633200-120633400	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr7:120633200-120633800	Enhancers	Adipose Nuclei	Adipose
49	chr7:120633200-120633800	Enhancers	NHDF-Ad	bronchial
50	chr7:120633200-120634000	Weak transcription	Right Atrium	heart

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