Variant report

Variant	rs10249885
Chromosome Location	chr7:30662237-30662238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:30633094..30635716-chr7:30661966..30665507,3	MCF-7	breast:
2	chr7:30654894..30658885-chr7:30662192..30664478,3	K562	blood:

Variant related genes	Relation type
ENSG00000106105	Chromatin interaction
ENSG00000196295	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10227133	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10232372	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10233132	0.81[ASN][1000 genomes]
rs10237725	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10239660	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10243040	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265589	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10480088	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1074373	0.98[ASN][1000 genomes]
rs10951271	0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1141114	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11761080	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12532057	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533961	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13228758	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468402	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1558064	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875282	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16875285	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009662	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2214837	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240401	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267710	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2270025	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2391870	0.81[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap]
rs3779250	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3807632	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722992	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4722999	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6462211	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6947982	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6970688	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6970807	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs929377	0.88[CHD][hapmap];0.80[GIH][hapmap]
rs9648369	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[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	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1016256	chr7:30649212-31163056	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1023120	chr7:30655070-31185096	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2761316	chr7:30655082-31166676	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv527038	chr7:30657467-31161945	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv916877	chr7:30661135-31154731	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10249885	AC005154.6	cis	lung	GTEx
rs10249885	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs10249885	FKBP9	cis	parietal	SCAN
rs10249885	NEUROD6	cis	parietal	SCAN
rs10249885	CRHR2	cis	parietal	SCAN
rs10249885	AC005154.6	cis	Esophagus Mucosa	GTEx
rs10249885	HOXA1	cis	cerebellum	SCAN
rs10249885	AC005154.6	cis	Nerve Tibial	GTEx
rs10249885	AC005154.6	cis	Thyroid	GTEx
rs10249885	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs10249885	AC005154.6	cis	Artery Tibial	GTEx
rs10249885	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs10249885	CREB5	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30636200-30689200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:30636600-30682800	Weak transcription	Stomach Mucosa	stomach
3	chr7:30637000-30676000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:30637200-30676200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:30637600-30675400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:30637600-30675400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:30637800-30675600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:30638000-30675800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:30638000-30675800	Strong transcription	A549	lung
10	chr7:30638000-30676000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:30638000-30676200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:30638200-30675800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:30638200-30675800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr7:30638200-30675800	Strong transcription	Fetal Thymus	thymus
15	chr7:30638200-30676000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:30638200-30676000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:30638400-30664000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:30638400-30675800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr7:30638400-30675800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr7:30638400-30676000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr7:30638400-30676000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:30638400-30676000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr7:30638400-30676000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:30638400-30676000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:30638400-30676000	Strong transcription	Liver	Liver
26	chr7:30638400-30676200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:30638600-30675800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:30638600-30675800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr7:30638600-30676000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr7:30638800-30672800	Strong transcription	NHDF-Ad	bronchial
31	chr7:30638800-30675200	Strong transcription	K562	blood
32	chr7:30638800-30675600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:30639000-30669600	Strong transcription	Fetal Intestine Large	intestine
34	chr7:30639000-30676200	Strong transcription	Hela-S3	cervix
35	chr7:30639200-30664200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr7:30639600-30662600	Strong transcription	Primary B cells from cord blood	blood
37	chr7:30639600-30675800	Strong transcription	Adipose Nuclei	Adipose
38	chr7:30639800-30676000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:30640200-30676000	Strong transcription	Dnd41	blood
40	chr7:30641800-30675600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr7:30647800-30675400	Strong transcription	Placenta	Placenta
42	chr7:30647800-30676000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:30648000-30662400	Strong transcription	GM12878-XiMat	blood
44	chr7:30648200-30675800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:30651400-30662600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:30651400-30663800	Strong transcription	Primary T cells from cord blood	blood
47	chr7:30651400-30676000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr7:30651600-30662400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr7:30652200-30669400	Strong transcription	NHLF	lung
50	chr7:30652400-30662400	Strong transcription	HSMMtube	muscle

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