Variant report

Variant	rs10085904
Chromosome Location	chr7:117834974-117834975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:117833281..117835799-chr7:117836785..117838521,2	MCF-7	breast:
2	chr7:117834706..117839817-chr7:117854613..117858941,5	K562	blood:
3	chr7:117685833..117688734-chr7:117834237..117836317,2	K562	blood:
4	chr7:117123377..117126210-chr7:117833079..117835993,3	K562	blood:
5	chr7:117794437..117796815-chr7:117833814..117836624,2	K562	blood:

Variant related genes	Relation type
ENSG00000106013	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1015782	0.83[EUR][1000 genomes]
rs10226152	0.93[EUR][1000 genomes]
rs10227326	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10229589	0.93[EUR][1000 genomes]
rs10241875	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10252627	0.81[EUR][1000 genomes]
rs10267938	0.86[EUR][1000 genomes]
rs10487390	0.93[EUR][1000 genomes]
rs1054032	0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1061731	0.91[CEU][hapmap];0.84[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs10953864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117254	0.89[EUR][1000 genomes]
rs11486992	0.85[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs11487110	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11543742	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11768889	0.80[EUR][1000 genomes]
rs11770353	0.89[EUR][1000 genomes]
rs11979012	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs12537795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666439	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12667103	0.84[EUR][1000 genomes]
rs12670769	0.80[EUR][1000 genomes]
rs13224397	0.80[EUR][1000 genomes]
rs13224733	0.91[EUR][1000 genomes]
rs17584359	0.80[EUR][1000 genomes]
rs194577	0.80[EUR][1000 genomes]
rs194578	0.80[EUR][1000 genomes]
rs194579	0.80[EUR][1000 genomes]
rs2058416	0.89[EUR][1000 genomes]
rs2058417	0.91[EUR][1000 genomes]
rs2058418	0.84[CEU][hapmap];0.80[MKK][hapmap];0.81[EUR][1000 genomes]
rs20598	0.80[EUR][1000 genomes]
rs2191920	0.89[EUR][1000 genomes]
rs2402322	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2896242	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs34029977	0.80[EUR][1000 genomes]
rs3802012	0.90[EUR][1000 genomes]
rs4141028	0.90[EUR][1000 genomes]
rs41900	0.86[EUR][1000 genomes]
rs41901	0.86[EUR][1000 genomes]
rs41902	0.86[EUR][1000 genomes]
rs41905	0.86[EUR][1000 genomes]
rs41906	0.86[EUR][1000 genomes]
rs41909	0.86[EUR][1000 genomes]
rs41910	0.84[EUR][1000 genomes]
rs41911	0.84[EUR][1000 genomes]
rs41915	0.83[EUR][1000 genomes]
rs41916	0.83[EUR][1000 genomes]
rs41926	0.83[EUR][1000 genomes]
rs41933	0.81[EUR][1000 genomes]
rs41934	0.83[EUR][1000 genomes]
rs41935	0.83[EUR][1000 genomes]
rs41938	0.83[EUR][1000 genomes]
rs41939	0.83[EUR][1000 genomes]
rs41945	0.83[EUR][1000 genomes]
rs41946	0.80[EUR][1000 genomes]
rs41947	0.80[EUR][1000 genomes]
rs41948	0.80[EUR][1000 genomes]
rs41949	0.80[EUR][1000 genomes]
rs41950	0.80[EUR][1000 genomes]
rs41951	0.80[EUR][1000 genomes]
rs41952	0.80[EUR][1000 genomes]
rs41953	0.80[EUR][1000 genomes]
rs41954	0.80[EUR][1000 genomes]
rs41955	0.80[EUR][1000 genomes]
rs41956	0.80[EUR][1000 genomes]
rs41957	0.80[EUR][1000 genomes]
rs41958	0.80[EUR][1000 genomes]
rs41961	0.80[EUR][1000 genomes]
rs41963	0.80[EUR][1000 genomes]
rs41964	0.80[EUR][1000 genomes]
rs41967	0.80[EUR][1000 genomes]
rs41969	0.80[EUR][1000 genomes]
rs41970	0.80[EUR][1000 genomes]
rs41977	0.80[EUR][1000 genomes]
rs41979	0.80[EUR][1000 genomes]
rs41980	0.80[EUR][1000 genomes]
rs41982	0.80[EUR][1000 genomes]
rs41984	0.80[EUR][1000 genomes]
rs41986	0.80[EUR][1000 genomes]
rs41987	0.80[EUR][1000 genomes]
rs41988	0.80[EUR][1000 genomes]
rs41990	0.80[EUR][1000 genomes]
rs41991	0.80[EUR][1000 genomes]
rs41993	0.80[EUR][1000 genomes]
rs42234	0.80[EUR][1000 genomes]
rs42376	0.80[EUR][1000 genomes]
rs4535672	0.80[EUR][1000 genomes]
rs4727865	0.80[EUR][1000 genomes]
rs5002232	0.81[EUR][1000 genomes]
rs5002233	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6466648	0.83[EUR][1000 genomes]
rs6466650	0.81[EUR][1000 genomes]
rs68189275	0.80[EUR][1000 genomes]
rs6942513	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs6944524	0.93[EUR][1000 genomes]
rs6946855	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs6948096	0.93[EUR][1000 genomes]
rs6956486	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964911	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs6965144	0.93[EUR][1000 genomes]
rs769435	0.81[MKK][hapmap]
rs7779933	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786233	0.81[CEU][hapmap]
rs7796145	0.93[EUR][1000 genomes]
rs7796148	0.93[EUR][1000 genomes]
rs7797855	0.93[EUR][1000 genomes]
rs7799229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917761	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9655829	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]
rs9656259	0.83[EUR][1000 genomes]
rs9656260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979652	0.83[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs989899	0.89[EUR][1000 genomes]
rs992035	0.87[CEU][hapmap];0.84[EUR][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
rs10085904	LSM8	cis	multi-tissue	Pritchard
rs10085904	ANKRD7	cis	parietal	SCAN
rs10085904	ANKRD7	cis	cerebellum	SCAN
rs10085904	NAA38	cis	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117825000-117842200	Weak transcription	Aorta	Aorta
2	chr7:117825600-117835000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:117825600-117835600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:117825600-117837200	Weak transcription	Left Ventricle	heart
5	chr7:117825800-117836600	Weak transcription	Psoas Muscle	Psoas
6	chr7:117825800-117842600	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:117826000-117835200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:117828000-117835600	Weak transcription	NHEK	skin
9	chr7:117828400-117835800	Weak transcription	Brain Substantia Nigra	brain
10	chr7:117828400-117836000	Weak transcription	Fetal Kidney	kidney
11	chr7:117828800-117835400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:117828800-117838800	Weak transcription	Primary B cells from cord blood	blood
13	chr7:117829200-117835400	Weak transcription	Colonic Mucosa	Colon
14	chr7:117829800-117835600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:117829800-117840800	Weak transcription	Primary T cells from cord blood	blood
16	chr7:117830400-117835200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:117830400-117842400	Weak transcription	Fetal Lung	lung
18	chr7:117830600-117835600	Weak transcription	A549	lung
19	chr7:117831000-117835000	Strong transcription	Dnd41	blood
20	chr7:117831000-117835400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:117831200-117835200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:117831200-117835600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr7:117831200-117836000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:117831200-117842400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:117831400-117839800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:117832000-117835400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:117832200-117835400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:117832200-117836400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:117832600-117835600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr7:117832600-117836200	Weak transcription	Adipose Nuclei	Adipose
31	chr7:117832600-117836400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:117832800-117835000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:117832800-117842200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:117833000-117835000	Weak transcription	HMEC	breast
35	chr7:117833000-117837200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:117833000-117854000	Weak transcription	HSMM	muscle
37	chr7:117833200-117835200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:117833200-117835600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:117833200-117836200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:117833200-117837000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:117833400-117835200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr7:117833400-117835600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr7:117833400-117835600	Weak transcription	Liver	Liver
44	chr7:117833400-117835600	Weak transcription	GM12878-XiMat	blood
45	chr7:117833400-117842200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:117833600-117854000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:117833800-117835600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr7:117834000-117835800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr7:117834000-117836600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr7:117834000-117836800	Weak transcription	Primary monocytes fromperipheralblood	blood

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