Variant report

Variant	rs715207
Chromosome Location	chr6:88370957-88370958
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88370220..88371861-chr6:88394700..88396720,2	K562	blood:
2	chr6:88368493..88371498-chr6:88375456..88378461,3	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs16879704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16879736	0.89[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs28381470	0.83[EUR][1000 genomes]
rs28381475	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28381530	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41273297	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55909105	0.88[ASN][1000 genomes]
rs55985738	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56400749	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57573658	0.97[ASN][1000 genomes]
rs58060521	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59131518	0.88[EUR][1000 genomes]
rs59774543	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60082015	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60316099	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66502414	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66588280	0.85[EUR][1000 genomes]
rs66965134	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67575319	0.85[EUR][1000 genomes]
rs67700862	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67956402	0.83[EUR][1000 genomes]
rs67993159	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68082038	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6906734	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap]
rs6907107	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6924641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6932733	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72906514	0.86[EUR][1000 genomes]
rs72922577	0.83[EUR][1000 genomes]
rs72924341	0.91[ASN][1000 genomes]
rs72924342	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73498106	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7747792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7748286	0.88[EUR][1000 genomes]
rs7752473	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7753275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7760237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7769144	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7776049	0.85[EUR][1000 genomes]
rs8802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs9450782	0.82[EUR][1000 genomes]

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	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs715207	SFN	trans	brain	seeQTL
rs715207	SRSF12	cis	parietal	SCAN
rs715207	C6orf165	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:88312200-88371200	Weak transcription	NHEK	skin
5	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
6	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
7	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
9	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
11	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:88324000-88385000	Weak transcription	Gastric	stomach
14	chr6:88324200-88378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:88324200-88380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:88329800-88383200	Weak transcription	Lung	lung
17	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
18	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
19	chr6:88344400-88384800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:88346600-88373800	Weak transcription	Fetal Kidney	kidney
21	chr6:88346600-88376400	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:88347800-88378000	Weak transcription	Fetal Brain Female	brain
23	chr6:88348000-88385000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:88348600-88377600	Weak transcription	Brain Anterior Caudate	brain
25	chr6:88349200-88373200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr6:88349200-88381400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:88349400-88377800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:88349400-88385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:88349400-88397400	Weak transcription	Ovary	ovary
30	chr6:88355200-88379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:88356600-88380400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:88358200-88392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:88359800-88381000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:88361000-88380400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:88362200-88371800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:88363200-88371000	Weak transcription	Primary B cells from cord blood	blood
38	chr6:88363200-88395000	Weak transcription	Stomach Mucosa	stomach
39	chr6:88363400-88375800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:88364400-88373200	Weak transcription	Liver	Liver
41	chr6:88364400-88384800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:88364800-88376600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:88365000-88376600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:88365000-88390000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:88365400-88373400	Weak transcription	Fetal Intestine Small	intestine
46	chr6:88365400-88379800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:88366400-88371600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr6:88366400-88390000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:88366600-88390000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:88367000-88371600	Strong transcription	Primary T cells fromperipheralblood	blood

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