Variant report

Variant	rs3823287
Chromosome Location	chr6:2244721-2244722
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:2244606-2247054	K562	blood:	n/a	chr6:2246619-2246627 chr6:2246618-2246628 chr6:2246618-2246628 chr6:2246321-2246331 chr6:2246994-2247005 chr6:2246618-2246628 chr6:2246618-2246628
2	MAX	chr6:2244555-2247000	HepG2	liver:	n/a	n/a
3	ZEB1	chr6:2244538-2247191	HepG2	liver:	n/a	chr6:2245548-2245557 chr6:2245548-2245560 chr6:2245266-2245278
4	MXI1	chr6:2244598-2246758	SK-N-SH	brain:	n/a	n/a
5	MBD4	chr6:2244247-2245270	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:2231926..2234637-chr6:2242249..2244795,3	MCF-7	breast:
2	chr6:2235011..2238207-chr6:2241335..2245707,5	K562	blood:
3	chr17:56707904..56710357-chr6:2244331..2245870,2	MCF-7	breast:
4	chr6:2235665..2237957-chr6:2241692..2244945,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRNIP1-3	chr6:2244111-2245348	ENSG00000246005

Variant related genes	Relation type
GMDS-AS1	TF binding region
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11242758	0.85[ASN][1000 genomes]
rs11961324	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11962550	0.82[ASN][1000 genomes]
rs11963138	1.00[ASN][1000 genomes]
rs11963529	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12191002	0.85[ASN][1000 genomes]
rs12661136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196306	0.99[ASN][1000 genomes]
rs13217030	1.00[ASN][1000 genomes]
rs2295008	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2450299	0.96[ASN][1000 genomes]
rs2450304	1.00[ASN][1000 genomes]
rs2450307	0.96[ASN][1000 genomes]
rs2450310	0.87[ASN][1000 genomes]
rs2479001	0.96[ASN][1000 genomes]
rs2479002	0.96[ASN][1000 genomes]
rs2479004	0.96[ASN][1000 genomes]
rs2479008	0.87[ASN][1000 genomes]
rs2479011	0.85[ASN][1000 genomes]
rs2479014	0.85[ASN][1000 genomes]
rs2505657	0.89[ASN][1000 genomes]
rs2505658	0.89[ASN][1000 genomes]
rs2505659	0.96[ASN][1000 genomes]
rs2505660	0.96[ASN][1000 genomes]
rs2505661	0.96[ASN][1000 genomes]
rs2505662	0.93[ASN][1000 genomes]
rs2505663	0.96[ASN][1000 genomes]
rs2505666	0.96[ASN][1000 genomes]
rs2505667	0.98[ASN][1000 genomes]
rs2505670	0.83[ASN][1000 genomes]
rs2505671	0.85[ASN][1000 genomes]
rs2505673	0.85[ASN][1000 genomes]
rs2505677	0.89[ASN][1000 genomes]
rs2505678	0.89[ASN][1000 genomes]
rs36016883	0.84[ASN][1000 genomes]
rs3778568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800185	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800187	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55992523	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56196406	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6596879	0.85[ASN][1000 genomes]
rs72830182	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72830184	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7754950	1.00[ASN][1000 genomes]
rs9328087	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs9378327	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9378686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378692	0.98[ASN][1000 genomes]
rs9378693	0.98[ASN][1000 genomes]
rs9391946	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs9392373	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9392374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392375	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392377	1.00[ASN][1000 genomes]
rs9405550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS 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	46 gene(s)	inside rSNPs	diseases
5	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
10	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
17	nsv1026678	chr6:2230064-2261297	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a
18	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3823287	WRNIP1	cis	parietal	SCAN
rs3823287	LYRM4	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2232000-2244800	Weak transcription	Aorta	Aorta
2	chr6:2237800-2244800	Weak transcription	NHLF	lung
3	chr6:2238400-2245000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:2241400-2244800	Weak transcription	Psoas Muscle	Psoas
5	chr6:2242800-2245000	Weak transcription	Right Atrium	heart
6	chr6:2243200-2245000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:2243200-2246800	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr6:2243200-2246800	Active TSS	Gastric	stomach
9	chr6:2243400-2244800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:2243400-2244800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:2243600-2244800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr6:2243800-2244800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:2243800-2245000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr6:2244000-2245000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:2244200-2244800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr6:2244200-2244800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:2244200-2244800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:2244200-2244800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:2244200-2244800	Enhancers	Fetal Thymus	thymus
20	chr6:2244200-2245000	Enhancers	Placenta	Placenta
21	chr6:2244200-2245200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr6:2244200-2245200	Flanking Active TSS	GM12878-XiMat	blood
23	chr6:2244200-2245200	Flanking Active TSS	Hela-S3	cervix
24	chr6:2244200-2246600	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr6:2244200-2246600	Active TSS	Stomach Mucosa	stomach
26	chr6:2244200-2247000	Active TSS	Colonic Mucosa	Colon
27	chr6:2244400-2244800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:2244400-2244800	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:2244400-2244800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:2244400-2244800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:2244400-2244800	Enhancers	Brain Angular Gyrus	brain
32	chr6:2244400-2244800	Active TSS	Fetal Stomach	stomach
33	chr6:2244400-2244800	Flanking Bivalent TSS/Enh	HepG2	liver
34	chr6:2244400-2244800	Enhancers	K562	blood
35	chr6:2244400-2245000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:2244400-2245000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr6:2244400-2245000	Flanking Active TSS	HMEC	breast
38	chr6:2244400-2245000	Flanking Active TSS	Osteobl	bone
39	chr6:2244400-2245200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr6:2244400-2245200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr6:2244400-2245200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr6:2244400-2245200	Flanking Active TSS	NHEK	skin
43	chr6:2244400-2245400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:2244400-2245400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr6:2244400-2245600	Flanking Active TSS	Dnd41	blood
46	chr6:2244400-2246600	Active TSS	Small Intestine	intestine
47	chr6:2244400-2247000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:2244600-2244800	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr6:2244600-2244800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr6:2244600-2244800	Flanking Active TSS	H9 Cell Line	embryonic stem cell

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