Variant report

Variant	rs6937607
Chromosome Location	chr6:131604844-131604845
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1317667	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1322596	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs1570348	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17573187	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17651753	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17787964	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs35673664	1.00[ASN][1000 genomes]
rs3777487	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3777493	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3903759	0.90[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs55893652	0.87[EUR][1000 genomes]
rs56059672	0.88[EUR][1000 genomes]
rs56189731	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56318353	0.83[EUR][1000 genomes]
rs73631985	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73634710	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743894	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7754007	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492861	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv886665	chr6:131518894-131611309	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv830808	chr6:131521115-131735320	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv886666	chr6:131573433-131666295	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv965766	chr6:131603694-131605067	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6937607	VNN3	cis	parietal	SCAN
rs6937607	VNN1	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131571800-131614400	Weak transcription	Gastric	stomach
2	chr6:131572200-131613000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:131573600-131610400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:131580600-131606000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:131580800-131605000	Weak transcription	Fetal Heart	heart
6	chr6:131587400-131614400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:131590800-131610200	Weak transcription	Fetal Stomach	stomach
8	chr6:131591000-131614800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:131591400-131610600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:131597200-131613200	Weak transcription	Ovary	ovary
11	chr6:131601200-131612000	Weak transcription	HSMMtube	muscle
12	chr6:131602400-131607000	Enhancers	Fetal Intestine Large	intestine
13	chr6:131602600-131605200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:131602800-131605000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:131602800-131606400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr6:131602800-131612800	Weak transcription	HepG2	liver
17	chr6:131602800-131613200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:131603000-131605000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:131603000-131605200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:131603000-131606000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:131603000-131606000	Weak transcription	Fetal Brain Female	brain
22	chr6:131603000-131606200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:131603200-131605000	Enhancers	Fetal Intestine Small	intestine
24	chr6:131603200-131605400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr6:131603200-131605600	Enhancers	Brain Anterior Caudate	brain
26	chr6:131603200-131606000	Weak transcription	Aorta	Aorta
27	chr6:131603200-131606400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:131603200-131606400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:131603200-131607800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr6:131603200-131607800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:131603200-131608000	Weak transcription	Fetal Lung	lung
32	chr6:131603200-131613000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:131603200-131613200	Weak transcription	Left Ventricle	heart
34	chr6:131603200-131613800	Weak transcription	Right Atrium	heart
35	chr6:131603200-131614600	Weak transcription	Lung	lung
36	chr6:131603400-131605000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:131603400-131606000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr6:131603400-131606000	Weak transcription	Fetal Thymus	thymus
39	chr6:131603400-131606400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr6:131603400-131606400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr6:131603400-131606400	Weak transcription	Dnd41	blood
42	chr6:131603400-131607000	Enhancers	Primary T cells from cord blood	blood
43	chr6:131603400-131611600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:131603400-131612000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:131603400-131612200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:131603400-131613000	Weak transcription	Adipose Nuclei	Adipose
47	chr6:131603400-131613400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:131603400-131613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:131603400-131613400	Weak transcription	Psoas Muscle	Psoas
50	chr6:131603400-131613600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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