Variant report

Variant	rs9655829
Chromosome Location	chr7:117825549-117825550
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:39677208..39679664-chr7:117824087..117825656,2	MCF-7	breast:
2	chr7:116897859..116900656-chr7:117824567..117826449,2	K562	blood:
3	chr7:117825039..117827152-chr7:120589846..120592123,2	MCF-7	breast:
4	chr7:117822159..117825807-chr7:117854196..117858736,4	K562	blood:
5	chr2:234775602..234777791-chr7:117824084..117825749,2	MCF-7	breast:
6	chr7:117824273..117825955-chr7:117864602..117866522,2	MCF-7	breast:
7	chr7:117825257..117827852-chr7:118309009..118311377,2	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction
ENSG00000106013	Chromatin interaction
ENSG00000224287	Chromatin interaction
ENSG00000171346	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10085904	0.85[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10226152	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10227326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10229589	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10241875	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10252627	0.88[EUR][1000 genomes]
rs10267938	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10487390	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054032	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061731	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953864	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1117254	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11486992	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11543742	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11770353	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11979012	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12112697	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs12537795	0.91[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12667103	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12673046	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13224733	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2041527	0.84[CEU][hapmap];0.83[MKK][hapmap];0.81[EUR][1000 genomes]
rs2041528	0.81[EUR][1000 genomes]
rs2058416	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2058417	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2191920	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2402322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802012	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141028	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41900	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41901	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41902	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41905	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41906	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41909	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41910	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41911	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41915	0.90[EUR][1000 genomes]
rs41916	0.90[EUR][1000 genomes]
rs41926	0.90[EUR][1000 genomes]
rs41933	0.88[EUR][1000 genomes]
rs41934	0.90[EUR][1000 genomes]
rs41935	0.90[EUR][1000 genomes]
rs41938	0.90[EUR][1000 genomes]
rs41939	0.90[EUR][1000 genomes]
rs41945	0.80[EUR][1000 genomes]
rs41960	0.84[EUR][1000 genomes]
rs5002233	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466650	0.84[EUR][1000 genomes]
rs6942513	0.83[CEU][hapmap]
rs6944524	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6948096	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956486	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6964911	0.91[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6965144	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779933	0.93[EUR][1000 genomes]
rs7796145	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7796148	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7797855	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7799229	0.91[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7806490	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917761	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9656260	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs979652	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9886333	0.82[EUR][1000 genomes]
rs989899	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9655829	LSM8	cis	multi-tissue	Pritchard
rs9655829	ANKRD7	cis	cerebellum	SCAN
rs9655829	NAA38	cis	lymphoblastoid	seeQTL
rs9655829	ANKRD7	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117822400-117825600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:117822600-117825800	Active TSS	Psoas Muscle	Psoas
3	chr7:117822800-117825600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:117822800-117825600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr7:117822800-117825600	Active TSS	A549	lung
6	chr7:117823000-117825800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:117823000-117825800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr7:117823000-117826000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr7:117823000-117826000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:117823200-117826000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:117823400-117825600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr7:117823400-117825800	Active TSS	Rectal Smooth Muscle	rectum
13	chr7:117823400-117826000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:117823400-117826000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr7:117823400-117826000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr7:117823400-117826000	Active TSS	Fetal Brain Female	brain
17	chr7:117823400-117826800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:117823600-117825600	Active TSS	NH-A	brain
19	chr7:117823600-117826600	Active TSS	K562	blood
20	chr7:117824400-117825800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr7:117824600-117825600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr7:117824600-117825600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:117824600-117825800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:117824600-117826000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr7:117824800-117825600	Flanking Active TSS	Fetal Lung	lung
26	chr7:117824800-117825600	Flanking Active TSS	HUVEC	blood vessel
27	chr7:117824800-117825800	Flanking Active TSS	Liver	Liver
28	chr7:117824800-117826000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr7:117824800-117826000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr7:117824800-117826000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:117824800-117826000	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr7:117824800-117829000	Weak transcription	Lung	lung
33	chr7:117824800-117829200	Weak transcription	Gastric	stomach
34	chr7:117824800-117832600	Weak transcription	Pancreas	Pancrea
35	chr7:117825000-117825600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:117825000-117825600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:117825000-117825600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr7:117825000-117825600	Flanking Active TSS	Osteobl	bone
39	chr7:117825000-117825800	Enhancers	Brain Cingulate Gyrus	brain
40	chr7:117825000-117826000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr7:117825000-117826000	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr7:117825000-117826000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:117825000-117826000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr7:117825000-117826000	Enhancers	Fetal Brain Male	brain
45	chr7:117825000-117826000	Enhancers	Small Intestine	intestine
46	chr7:117825000-117826200	Enhancers	Primary B cells from peripheral blood	blood
47	chr7:117825000-117826200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr7:117825000-117826600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:117825000-117827000	Weak transcription	Placenta	Placenta
50	chr7:117825000-117827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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