Variant report

Variant	rs12386764
Chromosome Location	chr7:4275676-4275677
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:4265084..4267850-chr7:4273909..4275894,2	K562	blood:
2	chr7:4274876..4277578-chr7:4279083..4281112,2	K562	blood:

Variant related genes	Relation type
ENSG00000146555	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10487575	0.85[CHD][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs10951486	0.85[CHD][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12386762	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12531029	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs12701504	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12701516	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13226493	0.82[ASW][hapmap];0.94[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13228974	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13229094	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13230364	1.00[CHB][hapmap]
rs13231488	0.90[EUR][1000 genomes]
rs13240660	1.00[CHB][hapmap]
rs13242033	0.86[EUR][1000 genomes]
rs13247068	0.82[ASW][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs2158722	1.00[CHB][hapmap]
rs2880459	1.00[CHB][hapmap]
rs34177767	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34670163	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34861141	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34931244	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35168770	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35399365	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35527356	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35863749	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35913974	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4723519	1.00[CEU][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4723528	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4723539	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4723545	0.81[EUR][1000 genomes]
rs56250749	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67819850	0.92[EUR][1000 genomes]
rs6946599	0.87[EUR][1000 genomes]
rs6966643	0.83[EUR][1000 genomes]
rs71527479	0.89[EUR][1000 genomes]
rs7781965	0.86[EUR][1000 genomes]
rs929371	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs929372	0.93[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs929373	0.93[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs929374	0.93[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv464274	chr7:3955516-4613607	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv464275	chr7:3955516-4613607	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv464276	chr7:3955516-4613607	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking 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	5 gene(s)	inside rSNPs	diseases
8	nsv464277	chr7:3955516-4613607	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv464278	chr7:3955516-4613607	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv605939	chr7:3955516-4613607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1019305	chr7:3991646-4276004	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv917252	chr7:4017819-4374090	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv527624	chr7:4027536-4424054	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv869540	chr7:4063875-4302040	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv518299	chr7:4116665-4286597	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats 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	1 gene(s)	inside rSNPs	diseases
16	nsv949581	chr7:4166659-4485938	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv1820543	chr7:4167991-4286597	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv887341	chr7:4167991-4298625	Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv887342	chr7:4182850-4293524	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1023367	chr7:4192258-4306053	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv887344	chr7:4211696-4393478	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv1029296	chr7:4243652-4276004	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv1030157	chr7:4272488-4311316	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12386764	WIPI2	cis	cerebellum	SCAN
rs12386764	MICALL2	cis	parietal	SCAN
rs12386764	C7orf50	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4235800-4287200	Weak transcription	Gastric	stomach
2	chr7:4244400-4283800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:4244800-4283800	Weak transcription	Right Ventricle	heart
4	chr7:4251000-4276600	Weak transcription	Aorta	Aorta
5	chr7:4255800-4284200	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:4256000-4283800	Weak transcription	Adipose Nuclei	Adipose
7	chr7:4256400-4283800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:4259800-4283600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:4261200-4285000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:4263800-4281200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:4265200-4283600	Weak transcription	Fetal Lung	lung
12	chr7:4266200-4279200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:4267000-4276000	Weak transcription	Spleen	Spleen
14	chr7:4267800-4281200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:4267800-4284400	Weak transcription	Fetal Brain Female	brain
16	chr7:4268000-4277200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:4268000-4291800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:4268200-4284000	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:4269200-4282600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:4271000-4283400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:4272800-4282600	Strong transcription	Fetal Stomach	stomach
22	chr7:4274000-4277000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:4274000-4279200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:4274400-4275800	Enhancers	HepG2	liver
25	chr7:4274600-4281400	Weak transcription	Pancreas	Pancrea
26	chr7:4274800-4277000	Weak transcription	Fetal Intestine Small	intestine
27	chr7:4274800-4277200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:4275400-4277200	Weak transcription	Lung	lung
29	chr7:4275600-4277000	Weak transcription	Fetal Intestine Large	intestine
30	chr7:4275600-4287800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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