Variant report

Variant	rs2528916
Chromosome Location	chr7:22319825-22319826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10227259	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs10242605	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10242851	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10268485	0.88[JPT][hapmap]
rs10276593	0.80[JPT][hapmap]
rs10499545	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs11975330	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11980801	0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap]
rs12333620	0.81[JPT][hapmap]
rs12534599	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs13239365	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs1345252	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs1543886	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs1568571	0.80[JPT][hapmap]
rs1568572	0.80[JPT][hapmap]
rs1636895	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17146447	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs17146497	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1798803	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158877	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2256891	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2528644	0.87[ASN][1000 genomes]
rs2528913	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2528914	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2528917	0.90[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2528918	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686469	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2686499	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2686528	0.93[CHB][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs34078437	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62447068	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779510	0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7796489	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs7798671	0.88[JPT][hapmap]
rs7799625	0.80[JPT][hapmap]
rs7805084	0.93[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830923	chr7:22316841-22494973	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2528916	DNAH11	cis	cerebellum	SCAN
rs2528916	CCDC126	cis	parietal	SCAN
rs2528916	HNRNPA2B1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:22262200-22329000	Weak transcription	Primary B cells from cord blood	blood
2	chr7:22278600-22325800	Weak transcription	Liver	Liver
3	chr7:22282200-22364400	Weak transcription	Esophagus	oesophagus
4	chr7:22309200-22322400	Weak transcription	Primary T cells from cord blood	blood
5	chr7:22309600-22328600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:22309600-22329000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:22310000-22327000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:22310000-22329000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:22310000-22335600	Weak transcription	Pancreas	Pancrea
10	chr7:22310000-22343400	Weak transcription	Spleen	Spleen
11	chr7:22314200-22327600	Weak transcription	Fetal Intestine Large	intestine
12	chr7:22314800-22331600	Weak transcription	Fetal Intestine Small	intestine
13	chr7:22316600-22327200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:22317000-22321000	Weak transcription	Thymus	Thymus
15	chr7:22317000-22324200	Genic enhancers	Dnd41	blood
16	chr7:22317600-22327000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:22318400-22320800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:22318400-22321000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:22318400-22321000	Enhancers	NHEK	skin
20	chr7:22318800-22328200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:22318800-22329000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:22318800-22340200	Weak transcription	Stomach Mucosa	stomach
23	chr7:22319000-22321000	Strong transcription	HepG2	liver
24	chr7:22319000-22336000	Weak transcription	Lung	lung
25	chr7:22319200-22320200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:22319600-22320800	Strong transcription	Fetal Thymus	thymus

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