Variant report

Variant	rs10378
Chromosome Location	chr7:150501455-150501456
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150488420..150491696-chr7:150501354..150503794,3	MCF-7	breast:
2	chr7:150495928..150500354-chr7:150501130..150505366,6	MCF-7	breast:
3	chr14:103799690..103801722-chr7:150499990..150502552,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100664	Chromatin interaction
ENSG00000106565	Chromatin interaction
ENSG00000002933	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1547958	1.00[JPT][hapmap]
rs17197782	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805123	1.00[JPT][hapmap]
rs28360734	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28508254	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28592021	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907948	1.00[JPT][hapmap]
rs2968854	1.00[JPT][hapmap]
rs2968856	1.00[JPT][hapmap]
rs2968863	1.00[JPT][hapmap]
rs2968864	1.00[JPT][hapmap]
rs57543564	0.86[ASN][1000 genomes]
rs62490434	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62490441	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62492366	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714883	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877120	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10378	CNTNAP2	cis	parietal	SCAN
rs10378	TMEM176A	cis	lymphoblastoid	seeQTL
rs10378	ZNF862	cis	cerebellum	SCAN
rs10378	TMEM176B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150498800-150501600	Enhancers	Placenta	Placenta
2	chr7:150498800-150502800	Weak transcription	Gastric	stomach
3	chr7:150498800-150503000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:150499400-150503000	Strong transcription	Ovary	ovary
5	chr7:150499600-150501800	Weak transcription	Pancreas	Pancrea
6	chr7:150499600-150502800	Weak transcription	Esophagus	oesophagus
7	chr7:150499800-150501800	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr7:150499800-150502600	Weak transcription	Brain Anterior Caudate	brain
9	chr7:150500200-150503000	Weak transcription	Brain Substantia Nigra	brain
10	chr7:150500400-150501600	Enhancers	Left Ventricle	heart
11	chr7:150500400-150501800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
12	chr7:150500400-150502600	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:150500600-150502800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr7:150500600-150503600	Weak transcription	Stomach Mucosa	stomach
15	chr7:150501000-150502200	Weak transcription	Right Ventricle	heart
16	chr7:150501000-150502600	Strong transcription	Colonic Mucosa	Colon
17	chr7:150501000-150502800	Strong transcription	Fetal Intestine Small	intestine
18	chr7:150501000-150502800	Strong transcription	Fetal Muscle Leg	muscle
19	chr7:150501000-150502800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:150501000-150502800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr7:150501000-150503000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:150501000-150503600	Strong transcription	Fetal Intestine Large	intestine
23	chr7:150501200-150501800	Genic enhancers	Liver	Liver
24	chr7:150501400-150501600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:150501400-150502000	ZNF genes & repeats	Spleen	Spleen
26	chr7:150501400-150502600	Strong transcription	Small Intestine	intestine
27	chr7:150501400-150502800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr7:150501400-150503400	ZNF genes & repeats	Adipose Nuclei	Adipose
29	chr7:150501400-150503400	ZNF genes & repeats	Fetal Stomach	stomach
30	chr7:150501400-150503600	Strong transcription	Rectal Mucosa Donor 31	rectum

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