Variant report

Variant	rs3800043
Chromosome Location	chr6:1764324-1764325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1762522..1764369-chr6:1837443..1839225,2	MCF-7	breast:
2	chr6:1762365..1765398-chr6:1767554..1769715,3	K562	blood:
3	chr6:1606384..1611793-chr6:1762059..1766159,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1013303	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1040528	0.90[CHB][hapmap]
rs1040530	0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs12200248	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs3734739	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs3734740	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs3734741	0.89[ASN][1000 genomes]
rs3800031	0.90[CHB][hapmap]
rs3800032	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs3800033	0.90[ASN][1000 genomes]
rs3800034	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs3800035	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs3800036	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs3800037	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs3800038	1.00[CEU][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes]
rs3800040	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3823262	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs4140588	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs4546532	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs4959155	0.89[ASN][1000 genomes]
rs4959605	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs6596850	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6596853	0.90[ASN][1000 genomes]
rs6596854	0.94[CHB][hapmap]
rs6596855	0.86[CHB][hapmap]
rs66477179	0.89[ASN][1000 genomes]
rs67800638	0.89[ASN][1000 genomes]
rs6911480	0.90[ASN][1000 genomes]
rs6912189	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6914704	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs6916153	0.95[ASN][1000 genomes]
rs6916760	0.86[ASN][1000 genomes]
rs6933551	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs6935246	0.86[CHB][hapmap]
rs742536	0.90[CHB][hapmap];0.94[ASN][1000 genomes]
rs761148	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs7740666	0.90[ASN][1000 genomes]
rs7749846	0.88[ASN][1000 genomes]
rs7753928	0.90[ASN][1000 genomes]
rs9391929	0.90[ASN][1000 genomes]
rs9392332	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs9392336	0.90[CHB][hapmap]

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	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv600809	chr6:1732741-1775436	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3800043	CRYL1	trans	lymphoblastoid	seeQTL
rs3800043	TUBB2B	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1738400-1768200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:1749800-1779000	Weak transcription	Aorta	Aorta
3	chr6:1751200-1780400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:1757000-1766000	Weak transcription	Right Atrium	heart
5	chr6:1757200-1766800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:1757200-1770600	Weak transcription	Lung	lung
7	chr6:1758600-1771400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:1758800-1767800	Weak transcription	Small Intestine	intestine
9	chr6:1761000-1768400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:1761600-1767400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:1762200-1765000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:1762600-1767800	Weak transcription	Brain Substantia Nigra	brain
13	chr6:1762600-1770600	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:1762800-1764400	Enhancers	Pancreas	Pancrea
15	chr6:1762800-1767800	Weak transcription	Fetal Intestine Large	intestine
16	chr6:1762800-1801600	Weak transcription	Colonic Mucosa	Colon
17	chr6:1763000-1765800	Weak transcription	Fetal Intestine Small	intestine
18	chr6:1763000-1766200	Weak transcription	Gastric	stomach
19	chr6:1763000-1767000	Weak transcription	Osteobl	bone
20	chr6:1763000-1792600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:1763200-1766000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:1763400-1764400	Enhancers	Placenta	Placenta
23	chr6:1763400-1764400	Enhancers	HUVEC	blood vessel
24	chr6:1763600-1764400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:1763600-1764400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr6:1763600-1765400	Weak transcription	Stomach Mucosa	stomach
27	chr6:1763600-1767000	Strong transcription	HepG2	liver
28	chr6:1763800-1767000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:1763800-1771600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:1764000-1765600	Enhancers	Fetal Lung	lung
31	chr6:1764000-1771400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:1764000-1773600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:1764200-1764400	Enhancers	Fetal Kidney	kidney
34	chr6:1764200-1766400	Weak transcription	HMEC	breast
35	chr6:1764200-1767000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:1764200-1767000	Weak transcription	Fetal Thymus	thymus
37	chr6:1764200-1767600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:1764200-1767600	Weak transcription	NHEK	skin
39	chr6:1764200-1767800	Weak transcription	GM12878-XiMat	blood
40	chr6:1764200-1768000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:1764200-1771400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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