Variant report

Variant	rs11808846
Chromosome Location	chr1:212943581-212943582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212943211..212944907-chr1:212962343..212965206,2	K562	blood:

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000117697	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10127512	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10127703	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10127756	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1046083	0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10863988	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10863997	0.84[CHB][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11120006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120007	0.81[ASN][1000 genomes]
rs11120010	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120017	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11120018	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120029	0.90[GIH][hapmap]
rs11556187	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11800642	0.81[ASN][1000 genomes]
rs11806535	0.83[ASN][1000 genomes]
rs11809232	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11809382	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11811017	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12125867	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12128410	0.90[GIH][hapmap]
rs12128903	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12129465	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12133174	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12137768	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12145131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12402370	0.88[ASN][1000 genomes]
rs12404618	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12404885	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12409787	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13376317	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13376383	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13376390	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1507357	0.84[CHB][hapmap];0.93[GIH][hapmap];0.80[MKK][hapmap];0.83[ASN][1000 genomes]
rs1507358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1532951	0.90[GIH][hapmap]
rs17019726	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs1857971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135823	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2174780	0.81[ASN][1000 genomes]
rs2174781	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271148	0.84[CHB][hapmap];0.90[GIH][hapmap];0.81[ASN][1000 genomes]
rs28872849	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34110137	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3738798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738803	0.93[GIH][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55840547	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56088044	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56243109	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57449384	0.88[ASN][1000 genomes]
rs58203936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59231663	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60308869	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61736926	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540760	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6540762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6657089	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664049	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6665365	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6670648	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6671866	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6687672	0.84[CHB][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6688238	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6694190	0.88[CEU][hapmap]
rs6694448	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6700204	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6702101	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73081830	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73081853	0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73081902	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73083705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083707	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73083727	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73083731	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73083743	0.86[ASN][1000 genomes]
rs73083749	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7516312	0.84[CHB][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7527216	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7536456	0.98[EUR][1000 genomes]
rs7537598	0.90[ASN][1000 genomes]
rs7538755	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7546754	0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7550288	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7552880	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7552899	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1005983	chr1:212917531-212947521	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11808846	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs11808846	IL20	cis	cerebellum	SCAN
rs11808846	SNORA16B	cis	cerebellum	SCAN
rs11808846	NSL1	cis	parietal	SCAN
rs11808846	SLC30A1	cis	parietal	SCAN
rs11808846	BATF3	cis	cerebellum	SCAN
rs11808846	TATDN3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212901400-212954000	Weak transcription	NH-A	brain
4	chr1:212902600-212943600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:212923600-212956200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:212923800-212947200	Weak transcription	A549	lung
9	chr1:212923800-212957600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:212923800-212964200	Weak transcription	HMEC	breast
11	chr1:212924000-212954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:212926600-212954200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:212926800-212947800	Weak transcription	NHDF-Ad	bronchial
15	chr1:212926800-212948000	Weak transcription	Osteobl	bone
16	chr1:212926800-212954200	Weak transcription	Hela-S3	cervix
17	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
18	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:212928400-212954000	Weak transcription	Fetal Brain Male	brain
20	chr1:212928400-212956200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:212928600-212947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:212928600-212954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:212929000-212947800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:212934200-212952400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:212936600-212950600	Weak transcription	Placenta	Placenta
26	chr1:212936600-212954800	Weak transcription	Left Ventricle	heart
27	chr1:212936600-212956000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:212936600-212956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:212936600-212956200	Weak transcription	Thymus	Thymus
30	chr1:212936600-212959800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:212936600-212960200	Weak transcription	Lung	lung
32	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
33	chr1:212937000-212944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:212938800-212946400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:212938800-212946600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:212939400-212956200	Weak transcription	Fetal Stomach	stomach
37	chr1:212939600-212946200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:212940000-212945600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:212940200-212944200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:212940600-212943800	ZNF genes & repeats	Dnd41	blood
41	chr1:212941200-212944400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
43	chr1:212941600-212943600	ZNF genes & repeats	Liver	Liver
44	chr1:212941600-212945600	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr1:212941600-212945600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
46	chr1:212941600-212945600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr1:212941800-212943600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:212941800-212943600	ZNF genes & repeats	Brain Anterior Caudate	brain
49	chr1:212941800-212944000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
50	chr1:212941800-212944200	ZNF genes & repeats	Primary T cells from cord blood	blood

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