Variant report

Variant	rs16956838
Chromosome Location	chr15:31819695-31819696
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31819613..31821709-chr15:31823051..31825388,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1075232	0.81[AMR][1000 genomes]
rs11858516	0.84[ASN][1000 genomes]
rs12438318	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs12438482	0.92[ASN][1000 genomes]
rs12440108	0.86[ASN][1000 genomes]
rs12441163	0.86[ASN][1000 genomes]
rs16956707	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs16956797	0.86[ASN][1000 genomes]
rs16956801	0.86[ASN][1000 genomes]
rs57491435	0.86[ASN][1000 genomes]
rs60333545	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166243	0.86[ASN][1000 genomes]
rs72724993	0.86[ASN][1000 genomes]
rs72724997	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv903845	chr15:31751664-31939001	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2422205	chr15:31808878-32375021	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv2422269	chr15:31808878-32375021	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv2422351	chr15:31808878-32375021	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv2422455	chr15:31808878-32375021	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs16956838	CHRFAM7A	cis	multi-tissue	Pritchard
rs16956838	RP11-932O9.7	cis	Artery Tibial	GTEx
rs16956838	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs16956838	RP11-932O9.9	cis	lung	GTEx
rs16956838	RP11-932O9.7	cis	Heart Left Ventricle	GTEx
rs16956838	RP11-932O9.7	cis	lung	GTEx
rs16956838	CHRNA7	cis	lung	GTEx
rs16956838	CHRNA7	cis	Artery Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31782400-31821000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:31802600-31825200	Weak transcription	Fetal Brain Female	brain
3	chr15:31810600-31821200	Weak transcription	Colonic Mucosa	Colon
4	chr15:31811400-31821200	Weak transcription	Pancreas	Pancrea
5	chr15:31814400-31820400	Strong transcription	Brain Inferior Temporal Lobe	brain
6	chr15:31815200-31823600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:31815600-31821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:31816000-31823200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:31816400-31823400	Weak transcription	Right Ventricle	heart
10	chr15:31816600-31820200	Strong transcription	Brain Cingulate Gyrus	brain
11	chr15:31817000-31820000	Strong transcription	Brain Substantia Nigra	brain
12	chr15:31817000-31820400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:31817000-31820600	Strong transcription	Brain Angular Gyrus	brain
14	chr15:31817000-31822800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:31818600-31820400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr15:31818800-31820200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:31818800-31821600	Weak transcription	Ovary	ovary
18	chr15:31819000-31820200	Enhancers	Fetal Muscle Trunk	muscle
19	chr15:31819200-31819800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:31819200-31820000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:31819200-31820000	Enhancers	Left Ventricle	heart
22	chr15:31819200-31820200	Enhancers	Spleen	Spleen
23	chr15:31819400-31819800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr15:31819400-31819800	Active TSS	Adipose Nuclei	Adipose
25	chr15:31819400-31820000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr15:31819400-31820200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:31819400-31820200	Enhancers	H9 Cell Line	embryonic stem cell
28	chr15:31819400-31820200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr15:31819600-31819800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:31819600-31820200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr15:31819600-31821800	Weak transcription	Brain Anterior Caudate	brain
32	chr15:31819600-31822000	Genic enhancers	Brain Hippocampus Middle	brain

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