Variant report

Variant	rs11609986
Chromosome Location	chr12:57635059-57635060
allele	A/G
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	CTCF	chr12:57634940-57635090	AoAF	blood vessel:	n/a	n/a
2	POLR2A	chr12:57632726-57635649	Raji	blood:	n/a	n/a
3	CTCF	chr12:57634940-57635090	WERI-Rb-1	eye:	n/a	n/a
4	CTCF	chr12:57634940-57635090	HFF	foreskin:	n/a	n/a
5	CTCF	chr12:57634940-57635090	HMF	breast:	n/a	n/a
6	CTCF	chr12:57634940-57635090	AG04450	lung:	n/a	n/a
7	SIN3A	chr12:57632041-57635117	H1-hESC	embryonic stem cell:	n/a	chr12:57633985-57633994 chr12:57635049-57635060 chr12:57634171-57634184 chr12:57632501-57632514 chr12:57632476-57632490
8	CTCF	chr12:57634960-57635110	HPF	lung:	n/a	n/a
9	CTCF	chr12:57634960-57635110	HAc	cerebellar:	n/a	n/a
10	SIN3AK20	chr12:57633923-57635212	MCF-7	breast:	n/a	n/a
11	MXI1	chr12:57632428-57635914	IMR90	lung:	n/a	n/a
12	CTCF	chr12:57634980-57635130	NHEK	skin:	n/a	n/a
13	CTCF	chr12:57634920-57635070	HEK293	kidney:	n/a	n/a
14	MAX	chr12:57633758-57635202	MCF-7	breast:	n/a	chr12:57634557-57634566 chr12:57633960-57633969 chr12:57634323-57634333
15	CTCF	chr12:57635040-57635190	A549	lung:	n/a	n/a
16	MXI1	chr12:57632140-57636615	SK-N-SH	brain:	n/a	n/a
17	MAX	chr12:57632726-57635084	A549	lung:	n/a	chr12:57634557-57634566 chr12:57633323-57633333 chr12:57633960-57633969 chr12:57634323-57634333
18	MXI1	chr12:57634220-57635091	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr12:57634828-57635105	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr12:57634980-57635130	GM12867	blood:	n/a	n/a
21	CTCF	chr12:57634940-57635090	GM12864	blood:	n/a	n/a
22	CTCF	chr12:57634940-57635090	HCFaa	heart:	n/a	n/a
23	CTCF	chr12:57635020-57635170	GM12865	blood:	n/a	n/a
24	CTCF	chr12:57631820-57635252	SK-N-SH	brain:	n/a	chr12:57634460-57634468 chr12:57633007-57633016 chr12:57633003-57633016 chr12:57633002-57633018 chr12:57634530-57634538 chr12:57633004-57633014 chr12:57633001-57633019 chr12:57632996-57633017
25	REST	chr12:57632540-57635232	H1-neurons	neurons:	n/a	chr12:57632547-57632556 chr12:57633984-57633994 chr12:57634777-57634790 chr12:57633753-57633773 chr12:57634171-57634184 chr12:57632550-57632563 chr12:57635049-57635062 chr12:57632577-57632597
26	CTCF	chr12:57632349-57635195	A549	lung:	n/a	chr12:57634460-57634468 chr12:57633007-57633016 chr12:57633003-57633016 chr12:57633002-57633018 chr12:57634530-57634538 chr12:57633004-57633014 chr12:57633001-57633019 chr12:57632996-57633017
27	POLR2A	chr12:57631159-57635422	H1-neurons	neurons:	n/a	n/a
28	MAX	chr12:57632615-57635166	A549	lung:	n/a	chr12:57634557-57634566 chr12:57633323-57633333 chr12:57633960-57633969 chr12:57634323-57634333
29	CTBP2	chr12:57633488-57635717	H1-hESC	embryonic stem cell:	n/a	n/a
30	TBP	chr12:57634885-57635065	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZBTB7A	chr12:57632751-57635116	ECC-1	luminal epithelium:	n/a	chr12:57633002-57633011
32	CTCF	chr12:57634980-57635130	AG10803	skin:	n/a	n/a
33	CTCF	chr12:57634960-57635110	HCPEpiC	choroid plexus:	n/a	n/a
34	ELF1	chr12:57634186-57635178	MCF-7	breast:	n/a	chr12:57634502-57634515 chr12:57634402-57634411
35	CTCF	chr12:57634940-57635090	AG04449	skin:	n/a	n/a
36	CTCF	chr12:57634920-57635070	HPAF	blood vessel:	n/a	n/a
37	CTCF	chr12:57635000-57635150	HMF	breast:	n/a	n/a
38	CTCF	chr12:57634900-57635190	SK-N-SH_RA	brain:	n/a	n/a
39	CTCF	chr12:57634980-57635130	BE2_C	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57593061..57596040-chr12:57632973..57635946,3	K562	blood:
2	chr12:57634341..57637032-chr12:58003121..58004920,2	K562	blood:
3	chr12:57521132..57523355-chr12:57632415..57635225,2	K562	blood:
4	chr12:57586960..57589304-chr12:57634814..57636834,2	MCF-7	breast:
5	chr12:57503657..57505571-chr12:57633144..57635959,2	MCF-7	breast:
6	chr12:57633619..57639143-chr12:57853203..57857806,7	K562	blood:
7	chr12:57480680..57483745-chr12:57634924..57637654,3	MCF-7	breast:
8	chr12:57632502..57635395-chr12:58164755..58167639,2	MCF-7	breast:
9	chr12:57633994..57636075-chr12:57915508..57917447,2	MCF-7	breast:
10	chr12:57478737..57483929-chr12:57633097..57638164,8	MCF-7	breast:

Variant related genes	Relation type
NDUFA4L2	TF binding region
ENSG00000257921	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000221365	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10747777	0.96[CEU][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs10747778	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10783818	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10783819	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs10783820	0.90[EUR][1000 genomes]
rs10876976	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs11172156	0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs11172160	0.83[EUR][1000 genomes]
rs11172165	0.81[EUR][1000 genomes]
rs11172169	0.85[CEU][hapmap]
rs11172170	0.96[CEU][hapmap]
rs11172190	0.88[CEU][hapmap]
rs12296766	0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12310220	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12579911	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12812140	0.92[CEU][hapmap]
rs1798710	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs2063778	0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs3923885	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4075325	0.93[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4760192	0.82[EUR][1000 genomes]
rs4760193	0.88[EUR][1000 genomes]
rs4760236	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs4760308	0.96[CEU][hapmap]
rs4760348	0.96[CEU][hapmap]
rs4760356	0.81[EUR][1000 genomes]
rs481196	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs491750	0.81[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs533975	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs537482	0.81[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs543410	0.81[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap]
rs560048	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs575153	0.81[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs6581131	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6581134	0.81[ASW][hapmap];0.95[GIH][hapmap];0.87[EUR][1000 genomes]
rs6581135	0.88[EUR][1000 genomes]
rs6581136	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7133939	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7135142	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7298418	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7307059	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs7309659	0.81[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs7313824	0.87[EUR][1000 genomes]
rs7314266	0.90[EUR][1000 genomes]
rs7358684	0.93[EUR][1000 genomes]
rs7398058	0.96[CEU][hapmap]
rs7486863	0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs7977908	0.96[CEU][hapmap];0.90[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11609986	SILV	cis	parietal	SCAN
rs11609986	OR6C4	cis	parietal	SCAN
rs11609986	TSPAN31	cis	cerebellum	SCAN
rs11609986	ZNF385A	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57628600-57636200	Weak transcription	Hela-S3	cervix
2	chr12:57631600-57635600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:57631800-57635200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:57632000-57635200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
5	chr12:57632200-57635200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:57632800-57635400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:57632800-57635400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
8	chr12:57632800-57636400	Bivalent Enhancer	Fetal Heart	heart
9	chr12:57633600-57635200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
10	chr12:57633800-57635200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
11	chr12:57634000-57635200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
12	chr12:57634200-57635200	Flanking Active TSS	Fetal Brain Male	brain
13	chr12:57634200-57635200	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr12:57634200-57635600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:57634200-57635600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
16	chr12:57634400-57635200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:57634400-57635200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:57634400-57635200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
19	chr12:57634400-57635200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
20	chr12:57634400-57635200	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:57634400-57635400	Flanking Active TSS	HSMMtube	muscle
22	chr12:57634400-57635600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr12:57634400-57635800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:57634600-57635200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:57634600-57635200	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:57634600-57635400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:57634600-57635400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:57634600-57635400	Bivalent Enhancer	Esophagus	oesophagus
29	chr12:57634600-57635600	Enhancers	Lung	lung
30	chr12:57634600-57636200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
31	chr12:57634600-57636200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:57634600-57636200	Weak transcription	Ovary	ovary
33	chr12:57634600-57636200	Enhancers	Pancreas	Pancrea
34	chr12:57634600-57636400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:57634600-57636400	Bivalent Enhancer	Stomach Mucosa	stomach
36	chr12:57634600-57636600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:57634600-57636600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:57634600-57636600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:57634600-57636600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:57634600-57636600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr12:57634600-57636600	Bivalent Enhancer	Fetal Intestine Small	intestine
42	chr12:57634600-57636600	Bivalent Enhancer	Fetal Stomach	stomach
43	chr12:57634600-57636600	Enhancers	Gastric	stomach
44	chr12:57634600-57636600	Enhancers	Psoas Muscle	Psoas
45	chr12:57634600-57637800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:57634600-57638000	Bivalent Enhancer	Fetal Lung	lung
47	chr12:57634800-57635200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:57634800-57635200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
49	chr12:57634800-57635200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
50	chr12:57634800-57635200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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