Variant report

Variant	rs6433319
Chromosome Location	chr2:172830953-172830954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172749569..172751818-chr2:172827980..172831224,3	K562	blood:
2	chr2:172829487..172831818-chr2:172832495..172834513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10165126	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10167419	0.87[CEU][hapmap]
rs10174055	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10201430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10202823	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10930502	0.87[CEU][hapmap]
rs11757	0.87[CEU][hapmap]
rs12692973	0.87[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs12692974	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs12692978	0.93[ASW][hapmap];0.83[CEU][hapmap]
rs13004237	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13030911	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2165934	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770445	0.93[ASW][hapmap];0.83[CEU][hapmap];0.85[MEX][hapmap]
rs3770451	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs3770452	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs4668414	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs62182433	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6715929	0.87[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs6724337	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs6725388	0.92[CEU][hapmap]
rs6727017	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6731562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6745143	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs6750058	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6752812	0.92[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6754817	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs6758704	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs6759575	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs7563971	0.85[EUR][1000 genomes]
rs7564089	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7573003	0.87[CEU][hapmap]
rs7581072	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7586207	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs7602037	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7608403	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs908670	0.93[ASW][hapmap];0.83[CEU][hapmap];0.85[MEX][hapmap]
rs908671	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6433319	DYNC1I2	cis	cerebellum	SCAN
rs6433319	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs6433319	AC068039.4	cis	Nerve Tibial	GTEx
rs6433319	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6433319	AC068039.4	cis	lung	GTEx
rs6433319	AC068039.4	cis	Thyroid	GTEx
rs6433319	AC068039.4	cis	Esophagus Mucosa	GTEx
rs6433319	AC068039.4	cis	Whole Blood	GTEx
rs6433319	AC068039.4	cis	Heart Left Ventricle	GTEx
rs6433319	AC068039.4	cis	Stomach	GTEx
rs6433319	SLC25A12	cis	parietal	SCAN
rs6433319	AC068039.4	cis	Esophagus Muscularis	GTEx
rs6433319	SLC25A12	cis	cerebellum	SCAN
rs6433319	AC068039.4	cis	Muscle Skeletal	GTEx
rs6433319	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs6433319	SLC25A12	cis	Whole Blood	GTEx
rs6433319	MYO3B	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172780200-172840400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:172780400-172848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:172780600-172847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
5	chr2:172783600-172851000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:172796000-172855200	Weak transcription	Gastric	stomach
7	chr2:172796800-172832200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:172807400-172845400	Weak transcription	Spleen	Spleen
9	chr2:172808000-172847200	Weak transcription	Fetal Brain Female	brain
10	chr2:172808000-172849400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:172809800-172837800	Weak transcription	Esophagus	oesophagus
12	chr2:172810000-172862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:172811400-172846200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:172811800-172852200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:172811800-172855600	Weak transcription	Fetal Heart	heart
16	chr2:172812400-172845200	Weak transcription	Colonic Mucosa	Colon
17	chr2:172813000-172859200	Weak transcription	Fetal Brain Male	brain
18	chr2:172814000-172844400	Weak transcription	Pancreas	Pancrea
19	chr2:172815200-172835800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:172815400-172850000	Weak transcription	HSMMtube	muscle
21	chr2:172816800-172844200	Weak transcription	NHLF	lung
22	chr2:172817800-172833800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:172817800-172833800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:172817800-172845200	Weak transcription	Psoas Muscle	Psoas
25	chr2:172821000-172838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:172821000-172862800	Weak transcription	Brain Angular Gyrus	brain
27	chr2:172821400-172835000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:172821800-172831200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:172822000-172833800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:172822000-172835800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:172822600-172833800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:172822800-172835000	Strong transcription	Dnd41	blood
33	chr2:172823000-172833600	Weak transcription	Left Ventricle	heart
34	chr2:172823000-172835400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:172823000-172850400	Weak transcription	Right Ventricle	heart
36	chr2:172823200-172833400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:172823200-172835800	Weak transcription	Brain Germinal Matrix	brain
38	chr2:172823200-172843600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:172823800-172831000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:172823800-172833600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:172823800-172839800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:172823800-172842600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:172823800-172843800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:172823800-172844000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:172823800-172851200	Weak transcription	Fetal Kidney	kidney
46	chr2:172824000-172833000	Weak transcription	Fetal Intestine Large	intestine
47	chr2:172824000-172833600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:172824000-172836800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:172824000-172841000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:172824000-172841200	Weak transcription	Rectal Mucosa Donor 29	rectum

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