Variant report

Variant	rs697222
Chromosome Location	chr12:57435122-57435123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57434884..57436914-chr12:57470851..57473489,2	K562	blood:
2	chr12:57425387..57428930-chr12:57434090..57438010,3	K562	blood:
3	chr12:57432223..57435386-chr12:57441665..57445560,4	MCF-7	breast:
4	chr12:57424729..57426887-chr12:57432611..57435590,2	K562	blood:
5	chr12:57432807..57436296-chr12:57438112..57442005,3	K562	blood:
6	chr12:57432591..57435585-chr12:57443883..57445567,2	K562	blood:

Variant related genes	Relation type
ENSG00000166866	Chromatin interaction
ENSG00000166881	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10400412	0.83[ASN][1000 genomes]
rs10400555	0.83[ASN][1000 genomes]
rs1044939	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10506347	0.87[GIH][hapmap]
rs10506350	0.81[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10506351	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1072670	0.85[JPT][hapmap]
rs11832487	0.80[ASN][1000 genomes]
rs11834851	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs11834856	0.80[ASN][1000 genomes]
rs11836517	0.80[ASN][1000 genomes]
rs12099695	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12810024	0.87[GIH][hapmap]
rs12810837	0.81[ASN][1000 genomes]
rs12812499	0.81[ASN][1000 genomes]
rs12815538	0.80[ASN][1000 genomes]
rs12818342	0.80[ASN][1000 genomes]
rs12824682	0.80[ASN][1000 genomes]
rs12827039	0.80[ASN][1000 genomes]
rs1552245	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs17119301	0.81[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17119327	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17119330	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17119344	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119352	0.88[ASN][1000 genomes]
rs17119386	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17119388	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17119390	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119407	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs17119416	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs17119418	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1843311	0.80[ASN][1000 genomes]
rs1843312	0.80[ASN][1000 genomes]
rs1843313	0.80[ASN][1000 genomes]
rs2167306	0.80[ASN][1000 genomes]
rs2270736	0.80[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2270737	0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs2270739	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2279373	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2279743	0.81[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2291855	0.83[ASN][1000 genomes]
rs2371717	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs28589663	0.80[ASN][1000 genomes]
rs2888139	0.81[ASN][1000 genomes]
rs34186462	0.80[ASN][1000 genomes]
rs34253098	0.80[ASN][1000 genomes]
rs34359134	0.80[ASN][1000 genomes]
rs34762603	0.85[ASN][1000 genomes]
rs34969650	0.82[ASN][1000 genomes]
rs35034299	0.80[ASN][1000 genomes]
rs35243318	0.80[ASN][1000 genomes]
rs35493121	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3782329	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3782330	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3803018	0.81[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3894415	0.81[ASN][1000 genomes]
rs4016338	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4039	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4143085	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs56128678	0.90[ASN][1000 genomes]
rs56270558	0.90[ASN][1000 genomes]
rs56354404	0.90[ASN][1000 genomes]
rs57056392	0.89[ASN][1000 genomes]
rs57129030	0.80[ASN][1000 genomes]
rs57558853	0.83[ASN][1000 genomes]
rs58298943	0.81[ASN][1000 genomes]
rs58389529	0.88[ASN][1000 genomes]
rs60273384	0.82[ASN][1000 genomes]
rs60380217	0.80[ASN][1000 genomes]
rs61504157	0.89[ASN][1000 genomes]
rs67476535	0.82[ASN][1000 genomes]
rs67771054	0.80[ASN][1000 genomes]
rs67844278	0.81[ASN][1000 genomes]
rs68126184	0.81[ASN][1000 genomes]
rs7135297	0.85[ASN][1000 genomes]
rs7136770	0.81[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs71461303	0.81[ASN][1000 genomes]
rs72482268	0.81[ASN][1000 genomes]
rs7298475	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs73114426	0.83[ASN][1000 genomes]
rs73114428	0.83[ASN][1000 genomes]
rs73114434	0.83[ASN][1000 genomes]
rs73114436	0.83[ASN][1000 genomes]
rs73114437	0.88[ASN][1000 genomes]
rs73114446	0.88[ASN][1000 genomes]
rs73114452	0.88[ASN][1000 genomes]
rs73114457	0.90[ASN][1000 genomes]
rs73114459	0.90[ASN][1000 genomes]
rs73114467	0.90[ASN][1000 genomes]
rs73114468	0.90[ASN][1000 genomes]
rs73114472	0.90[ASN][1000 genomes]
rs73116494	0.85[ASN][1000 genomes]
rs73116501	0.85[ASN][1000 genomes]
rs73118413	0.82[ASN][1000 genomes]
rs73131120	0.83[ASN][1000 genomes]
rs733629	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs746049	0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7487948	0.80[ASN][1000 genomes]
rs754398	0.85[ASN][1000 genomes]
rs755221	0.90[ASN][1000 genomes]
rs7956166	0.80[ASN][1000 genomes]
rs7961920	0.81[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7962771	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7969312	0.80[ASN][1000 genomes]
rs7972615	0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs901068	0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899110	chr12:57422934-57472502	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs697222	MYL6	cis	parietal	SCAN
rs697222	KRT75	cis	parietal	SCAN
rs697222	SHMT2	cis	cerebellum	SCAN
rs697222	STAT6	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57416800-57439400	Strong transcription	Fetal Intestine Small	intestine
2	chr12:57417200-57441200	Weak transcription	Small Intestine	intestine
3	chr12:57419200-57439400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr12:57419800-57439600	Strong transcription	Fetal Intestine Large	intestine
5	chr12:57420000-57440000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr12:57420400-57471800	Weak transcription	Gastric	stomach
7	chr12:57421800-57441600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:57427400-57435400	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:57429000-57438000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr12:57432800-57436800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:57433000-57435400	Enhancers	Fetal Thymus	thymus
12	chr12:57433600-57440400	Weak transcription	Primary T cells from cord blood	blood
13	chr12:57433600-57440800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:57433800-57440400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:57434400-57435400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:57434400-57439200	Strong transcription	Colonic Mucosa	Colon
17	chr12:57434600-57435400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:57434600-57435400	Enhancers	Fetal Muscle Leg	muscle
19	chr12:57434600-57435400	Enhancers	Thymus	Thymus
20	chr12:57434600-57435400	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr12:57434800-57435200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:57434800-57440400	Weak transcription	Stomach Mucosa	stomach

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