Variant report

Variant	rs6938840
Chromosome Location	chr6:38304855-38304856
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	chr6:38302380..38305369-chr6:38307558..38309248,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10484930	0.88[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12055513	0.87[ASW][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs12524225	0.88[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12527432	0.81[CHD][hapmap]
rs12529549	0.82[ASN][1000 genomes]
rs12660215	1.00[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12660323	0.88[CHD][hapmap];0.80[ASN][1000 genomes]
rs12664994	0.81[JPT][hapmap]
rs13197522	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs16890552	0.88[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs16890561	0.82[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2395697	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28360643	0.82[EUR][1000 genomes]
rs36094313	0.80[EUR][1000 genomes]
rs4711531	0.84[CHD][hapmap]
rs4714139	0.84[CHD][hapmap]
rs4714145	0.85[JPT][hapmap]
rs57575973	0.91[ASN][1000 genomes]
rs57934228	0.82[ASN][1000 genomes]
rs59459724	0.80[ASN][1000 genomes]
rs60500173	0.81[ASN][1000 genomes]
rs60814959	0.82[EUR][1000 genomes]
rs6917308	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs714930	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs73422824	0.84[ASN][1000 genomes]
rs73422833	0.84[ASN][1000 genomes]
rs764347	0.91[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7771835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871184	0.88[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9349065	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs9349069	0.90[ASN][1000 genomes]
rs9349071	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9366956	0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9369046	0.82[ASN][1000 genomes]
rs9369047	0.88[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9369050	0.95[ASN][1000 genomes]
rs9369052	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9380734	0.81[ASN][1000 genomes]
rs9380735	0.90[ASN][1000 genomes]
rs9380736	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9394487	0.86[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6938840	SRSF3	cis	parietal	SCAN
rs6938840	TEAD3	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38278000-38310600	Weak transcription	Gastric	stomach
2	chr6:38278400-38305400	Weak transcription	Pancreas	Pancrea
3	chr6:38285000-38327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:38288000-38305600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:38291000-38305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:38291400-38317600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:38299200-38313400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:38299800-38317800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:38301600-38305800	Weak transcription	HSMM	muscle
10	chr6:38301600-38306800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:38301600-38313400	Weak transcription	Psoas Muscle	Psoas
12	chr6:38301600-38315800	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:38301600-38324600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:38301800-38310400	Weak transcription	Primary B cells from cord blood	blood
15	chr6:38301800-38313400	Weak transcription	Aorta	Aorta
16	chr6:38302000-38310400	Weak transcription	Primary T cells from cord blood	blood
17	chr6:38302000-38315800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:38302000-38318200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:38302200-38315800	Weak transcription	Brain Substantia Nigra	brain
20	chr6:38303600-38306800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:38303800-38305000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
22	chr6:38303800-38311000	Weak transcription	Left Ventricle	heart
23	chr6:38304000-38305000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:38304000-38310400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:38304400-38305600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:38304600-38305000	Enhancers	Colon Smooth Muscle	Colon
27	chr6:38304600-38305400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:38304600-38323000	Weak transcription	Ovary	ovary
29	chr6:38304800-38305000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:38304800-38305000	Enhancers	Fetal Brain Female	brain
31	chr6:38304800-38305000	Enhancers	Fetal Stomach	stomach
32	chr6:38304800-38305000	Enhancers	Stomach Smooth Muscle	stomach
33	chr6:38304800-38306200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:38304800-38306800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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