Variant report

Variant	rs4235862
Chromosome Location	chr6:71534078-71534079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10447360	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1084382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1084385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1084386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17763641	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2347624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs2460694	1.00[ASN][1000 genomes]
rs2504742	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2504746	1.00[ASN][1000 genomes]
rs6455376	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6455381	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740106	1.00[ASN][1000 genomes]
rs7750570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294880	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9346399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446297	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS 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	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4235862	TNKS	trans	parietal	SCAN
rs4235862	COL19A1	cis	cerebellum	SCAN
rs4235862	RIMS1	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71474600-71568800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:71492400-71563600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:71505600-71534400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:71506800-71570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:71508400-71543800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:71511600-71554600	Weak transcription	Dnd41	blood
7	chr6:71514800-71535200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:71514800-71548400	Weak transcription	Ovary	ovary
9	chr6:71516200-71534600	Weak transcription	Aorta	Aorta
10	chr6:71516200-71534600	Weak transcription	Left Ventricle	heart
11	chr6:71516200-71535000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:71516200-71538400	Weak transcription	Esophagus	oesophagus
13	chr6:71516200-71538600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:71516200-71546200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:71516400-71535600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:71516400-71562200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:71516400-71567600	Weak transcription	Pancreas	Pancrea
18	chr6:71516600-71543400	Weak transcription	Adipose Nuclei	Adipose
19	chr6:71516600-71567600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:71518400-71552400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:71520600-71538400	Weak transcription	Fetal Intestine Small	intestine
22	chr6:71522000-71558200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:71524600-71548200	Weak transcription	Psoas Muscle	Psoas
24	chr6:71531200-71543600	Weak transcription	Liver	Liver
25	chr6:71531200-71571000	Weak transcription	Stomach Mucosa	stomach
26	chr6:71532000-71543400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:71532400-71557200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:71533000-71567600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:71533200-71541200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:71533200-71545600	Weak transcription	Primary T cells from cord blood	blood
31	chr6:71533200-71547600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:71533200-71548000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:71533200-71557000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:71533400-71535600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:71533800-71534800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr6:71534000-71550200	Weak transcription	Primary B cells from cord blood	blood
37	chr6:71534000-71563200	Weak transcription	Primary B cells from peripheral blood	blood

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