Variant report

Variant	rs10486802
Chromosome Location	chr7:39723768-39723769
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr7:39722662-39724213	SK-N-SH	brain:	n/a	chr7:39724046-39724056
2	GATA3	chr7:39722794-39724248	SK-N-SH	brain:	n/a	chr7:39723605-39723615 chr7:39723884-39723900 chr7:39723887-39723896 chr7:39723884-39723900
3	TEAD4	chr7:39722797-39723949	SK-N-SH	brain:	n/a	chr7:39723275-39723284

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39723283..39725435-chr7:39727516..39730400,2	MCF-7	breast:
2	chr7:39719329..39722043-chr7:39722542..39724877,2	K562	blood:

Variant related genes	Relation type
RALA	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10231409	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770964	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12666517	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12668645	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17171616	0.89[JPT][hapmap]
rs17416875	0.89[JPT][hapmap]
rs17507811	0.88[JPT][hapmap]
rs17508585	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17508730	0.89[JPT][hapmap]
rs2107707	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs34821005	0.84[EUR][1000 genomes]
rs3779203	0.89[JPT][hapmap]
rs62454689	0.87[EUR][1000 genomes]
rs6462943	0.83[EUR][1000 genomes]
rs7796021	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7799721	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10486802	HECW1	cis	parietal	SCAN
rs10486802	RALA	cis	cerebellum	SCAN
rs10486802	C7orf11	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39700000-39728200	Weak transcription	Liver	Liver
2	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
3	chr7:39702000-39727400	Weak transcription	Fetal Intestine Large	intestine
4	chr7:39707200-39727200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:39707200-39730000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:39712800-39728400	Weak transcription	Pancreas	Pancrea
7	chr7:39714000-39736800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:39715000-39736600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:39715200-39725000	Weak transcription	Primary T cells from cord blood	blood
10	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
11	chr7:39716800-39727000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr7:39716800-39727000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:39716800-39727200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:39716800-39727400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:39716800-39728400	Weak transcription	Primary B cells from cord blood	blood
16	chr7:39716800-39729200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:39716800-39735600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:39717000-39727400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:39718200-39739800	Weak transcription	Spleen	Spleen
20	chr7:39719000-39727200	Weak transcription	Fetal Brain Female	brain
21	chr7:39719600-39724000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:39719600-39727600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr7:39719800-39728600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr7:39720000-39728600	Weak transcription	HepG2	liver
25	chr7:39720200-39728400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:39720600-39724200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:39720600-39724200	Enhancers	Adipose Nuclei	Adipose
28	chr7:39721000-39724200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:39721000-39724200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr7:39721000-39725000	Enhancers	NHLF	lung
31	chr7:39721000-39725600	Enhancers	Fetal Lung	lung
32	chr7:39721200-39724600	Enhancers	Primary hematopoietic stem cells	blood
33	chr7:39721200-39730400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:39721200-39738200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr7:39721400-39724000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr7:39721400-39726400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr7:39721400-39727800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:39721400-39730000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr7:39721400-39735800	Weak transcription	K562	blood
40	chr7:39721600-39726400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:39721800-39724000	Enhancers	HSMMtube	muscle
42	chr7:39721800-39736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr7:39721800-39736600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:39722000-39727600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr7:39722000-39737600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr7:39722400-39724200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr7:39722400-39725000	Enhancers	Fetal Heart	heart
48	chr7:39722600-39723800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr7:39722600-39723800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr7:39722600-39723800	Enhancers	Osteobl	bone

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