Variant report

Variant	rs41688
Chromosome Location	chr7:120633006-120633007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120446160..120448246-chr7:120632744..120634259,2	K562	blood:
2	chr7:120631360..120633454-chr7:120681264..120683155,2	K562	blood:
3	chr7:120631497..120633631-chr7:120731853..120734107,2	K562	blood:
4	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
5	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:
6	chr7:120631348..120633454-chr7:120680148..120684056,4	K562	blood:

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10085563	0.85[CEU][hapmap]
rs10252911	0.80[CHB][hapmap]
rs10258025	0.81[EUR][1000 genomes]
rs10272601	0.83[CHB][hapmap]
rs10464522	0.87[ASN][1000 genomes]
rs12706307	0.85[CEU][hapmap]
rs12706308	0.84[CEU][hapmap]
rs12706309	0.85[CEU][hapmap]
rs12706310	0.85[CEU][hapmap]
rs13881	0.85[CEU][hapmap]
rs1859316	0.80[CHB][hapmap]
rs193727	0.84[EUR][1000 genomes]
rs2074576	0.95[CEU][hapmap]
rs2074577	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2107276	0.80[CHB][hapmap]
rs2160010	0.85[CEU][hapmap]
rs2215786	0.85[CEU][hapmap]
rs2215789	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2244863	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244865	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2248890	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2525711	0.85[CEU][hapmap]
rs2525712	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525713	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525714	0.85[CEU][hapmap]
rs2525715	0.88[CEU][hapmap]
rs2525716	0.84[CEU][hapmap]
rs2525717	0.94[CEU][hapmap]
rs2525718	0.95[CEU][hapmap]
rs2525719	0.95[CEU][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525720	0.85[CEU][hapmap]
rs2525722	0.95[CEU][hapmap]
rs2525724	0.85[CEU][hapmap]
rs2525725	0.85[CEU][hapmap]
rs2525726	0.85[CEU][hapmap]
rs2525728	0.85[CEU][hapmap]
rs2525729	0.81[ASN][1000 genomes]
rs2525730	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2525733	0.85[CEU][hapmap]
rs2525734	0.85[CEU][hapmap]
rs2525735	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525736	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525737	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525738	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525739	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525740	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525741	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538485	0.85[CEU][hapmap]
rs2721326	0.85[CEU][hapmap]
rs2721336	0.85[CEU][hapmap]
rs2721337	0.85[CEU][hapmap]
rs2721340	0.85[CEU][hapmap]
rs2721345	0.85[CEU][hapmap]
rs2721350	0.84[CEU][hapmap]
rs2721351	0.95[CEU][hapmap]
rs2721354	0.89[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.81[ASN][1000 genomes]
rs2721358	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2721359	0.85[EUR][1000 genomes]
rs2721361	0.85[EUR][1000 genomes]
rs2721363	0.90[CEU][hapmap];0.94[CHB][hapmap];0.85[GIH][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721365	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721366	0.85[CEU][hapmap]
rs2721367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721368	0.85[CEU][hapmap]
rs2721370	0.85[CEU][hapmap]
rs2721372	0.95[CEU][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757556	0.83[CHB][hapmap]
rs3779386	0.80[CHB][hapmap]
rs3944026	0.84[CEU][hapmap]
rs41689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41690	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41691	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs41692	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs41693	0.84[EUR][1000 genomes]
rs41694	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs41695	0.84[EUR][1000 genomes]
rs41697	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs41703	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs41704	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4727917	0.89[CEU][hapmap]
rs4730988	0.85[CEU][hapmap]
rs6466764	0.85[CEU][hapmap]
rs6964344	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs6966297	0.85[CEU][hapmap]
rs6970871	0.85[CEU][hapmap]
rs6971619	0.86[ASN][1000 genomes]
rs6971854	0.80[CHB][hapmap]
rs6973457	0.85[CEU][hapmap]
rs6979247	0.80[CHB][hapmap]
rs7776721	0.80[CHB][hapmap]
rs7784837	0.85[CEU][hapmap]
rs7808593	0.85[CEU][hapmap]

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	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41688	FLJ21986	cis	multi-tissue	Pritchard
rs41688	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120627600-120633800	Active TSS	Stomach Smooth Muscle	stomach
2	chr7:120627800-120633200	Active TSS	Right Atrium	heart
3	chr7:120627800-120633600	Active TSS	Ovary	ovary
4	chr7:120627800-120633800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:120627800-120633800	Active TSS	Aorta	Aorta
6	chr7:120627800-120633800	Active TSS	Right Ventricle	heart
7	chr7:120628200-120633800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:120628800-120633600	Active TSS	NHLF	lung
9	chr7:120629400-120634000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:120629600-120635800	Weak transcription	Primary B cells from cord blood	blood
11	chr7:120629800-120633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:120630000-120633600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:120630000-120633600	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr7:120630000-120636400	Weak transcription	HMEC	breast
15	chr7:120630200-120633800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:120630200-120636200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:120630200-120636200	Weak transcription	Placenta	Placenta
18	chr7:120631200-120633800	Weak transcription	Left Ventricle	heart
19	chr7:120631200-120640400	Weak transcription	Brain Anterior Caudate	brain
20	chr7:120631400-120636200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:120632000-120633600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr7:120632000-120633600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:120632000-120633800	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:120632000-120633800	Weak transcription	Psoas Muscle	Psoas
25	chr7:120632000-120634800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:120632000-120636400	Weak transcription	Hela-S3	cervix
27	chr7:120632200-120633200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:120632200-120633200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr7:120632200-120633600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:120632200-120636600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:120632400-120633200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr7:120632400-120633800	Weak transcription	NH-A	brain
33	chr7:120632400-120634200	Transcr. at gene 5' and 3'	HSMM	muscle
34	chr7:120632400-120641400	Transcr. at gene 5' and 3'	K562	blood
35	chr7:120632600-120633400	Weak transcription	Fetal Stomach	stomach
36	chr7:120632600-120633800	Weak transcription	Fetal Muscle Leg	muscle
37	chr7:120632600-120634000	Enhancers	Colon Smooth Muscle	Colon
38	chr7:120632600-120634200	Enhancers	Fetal Lung	lung
39	chr7:120632600-120634600	Weak transcription	Fetal Heart	heart
40	chr7:120632600-120635000	Enhancers	Rectal Smooth Muscle	rectum
41	chr7:120632800-120633200	Flanking Active TSS	Osteobl	bone
42	chr7:120632800-120633600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:120632800-120634400	Enhancers	Fetal Kidney	kidney
44	chr7:120633000-120633200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr7:120633000-120633200	Flanking Active TSS	NHDF-Ad	bronchial
46	chr7:120633000-120633400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr7:120633000-120633400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:120633000-120633800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:120633000-120634000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:120633000-120634600	Enhancers	Monocytes-CD14+_RO01746	blood

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