Variant report

Variant	rs7628838
Chromosome Location	chr3:67505898-67505899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67498464..67501413-chr3:67503941..67505935,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs4258984	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4320072	0.92[ASW][hapmap]
rs4423787	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4455333	0.81[EUR][1000 genomes]
rs4479607	0.85[EUR][1000 genomes]
rs4856867	0.94[EUR][1000 genomes]
rs6548593	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6792584	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7616397	0.82[EUR][1000 genomes]
rs7645087	0.87[EUR][1000 genomes]
rs9810030	0.85[EUR][1000 genomes]
rs9815209	0.87[EUR][1000 genomes]
rs9818109	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9836548	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9851569	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873214	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv508221	chr3:67487240-67509429	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv3860	chr3:67493286-67517941	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7628838	SUCLG2	cis	multi-tissue	Pritchard
rs7628838	ATXN7	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67435600-67509800	Weak transcription	Ovary	ovary
2	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
3	chr3:67466600-67508400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:67471600-67518800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:67472000-67506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:67472000-67509800	Weak transcription	HSMM	muscle
7	chr3:67473400-67521000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:67473600-67542000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:67478200-67512200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:67482600-67527200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:67482600-67528600	Weak transcription	GM12878-XiMat	blood
12	chr3:67482800-67520800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:67482800-67533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:67484000-67511400	Weak transcription	Fetal Lung	lung
15	chr3:67486800-67506000	Weak transcription	Primary T cells from cord blood	blood
16	chr3:67487000-67518600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:67487800-67512200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:67488000-67544200	Weak transcription	A549	lung
19	chr3:67488400-67566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:67490200-67511800	Weak transcription	HSMMtube	muscle
21	chr3:67492200-67545400	Weak transcription	Fetal Intestine Small	intestine
22	chr3:67492400-67515400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:67492400-67516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:67498000-67534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:67499400-67512000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:67500800-67567000	Weak transcription	Pancreas	Pancrea
27	chr3:67501200-67533600	Weak transcription	Fetal Intestine Large	intestine
28	chr3:67504000-67559800	Weak transcription	Esophagus	oesophagus
29	chr3:67504400-67509800	Weak transcription	Liver	Liver
30	chr3:67504600-67510000	Weak transcription	Primary B cells from cord blood	blood
31	chr3:67504600-67518800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:67504800-67513400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:67505800-67508000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:67505800-67516200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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