Variant report

Variant	rs41691
Chromosome Location	chr7:120634636-120634637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120633517..120635365-chr7:120747821..120749395,2	K562	blood:
2	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
3	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:

Variant related genes	Relation type
ENSG00000212628	Chromatin interaction
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10229719	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10258025	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12672149	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13881	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs193727	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013083	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2013087	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2074576	0.90[CEU][hapmap]
rs2074577	0.85[CEU][hapmap]
rs2215786	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2215789	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244863	0.85[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525711	1.00[CEU][hapmap]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2525714	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2525715	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap]
rs2525717	1.00[CEU][hapmap]
rs2525718	0.90[CEU][hapmap]
rs2525719	0.90[CEU][hapmap]
rs2525720	1.00[CEU][hapmap]
rs2525722	0.94[CEU][hapmap]
rs2525724	1.00[CEU][hapmap]
rs2525725	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2525726	1.00[CEU][hapmap]
rs2525728	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2525731	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2525732	0.81[EUR][1000 genomes]
rs2525733	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2525734	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2525735	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2525736	0.81[EUR][1000 genomes]
rs2525738	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2525739	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2525740	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2525741	0.84[EUR][1000 genomes]
rs2721350	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2721351	0.89[CEU][hapmap]
rs2721358	0.84[EUR][1000 genomes]
rs2721359	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2721361	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2721366	1.00[CEU][hapmap]
rs2721368	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2721370	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2721372	0.90[CEU][hapmap]
rs2896299	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3944026	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41688	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs41689	0.84[EUR][1000 genomes]
rs41692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41693	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41695	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41703	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4727915	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4730985	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4730987	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6953795	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6966297	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6973457	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7789501	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7808535	0.84[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.87[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41691	SPAM1	cis	parietal	SCAN
rs41691	FLJ21986	cis	multi-tissue	Pritchard
rs41691	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120629600-120635800	Weak transcription	Primary B cells from cord blood	blood
2	chr7:120630000-120636400	Weak transcription	HMEC	breast
3	chr7:120630200-120636200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:120630200-120636200	Weak transcription	Placenta	Placenta
5	chr7:120631200-120640400	Weak transcription	Brain Anterior Caudate	brain
6	chr7:120631400-120636200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:120632000-120634800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:120632000-120636400	Weak transcription	Hela-S3	cervix
9	chr7:120632200-120636600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:120632400-120641400	Transcr. at gene 5' and 3'	K562	blood
11	chr7:120632600-120635000	Enhancers	Rectal Smooth Muscle	rectum
12	chr7:120633000-120636600	Weak transcription	HSMMtube	muscle
13	chr7:120633000-120636800	Enhancers	Liver	Liver
14	chr7:120633000-120636800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr7:120633200-120634800	Enhancers	Osteobl	bone
16	chr7:120633200-120636400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:120633400-120635200	Enhancers	Fetal Stomach	stomach
18	chr7:120633600-120635400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:120633600-120636200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:120633600-120636200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:120633600-120636200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr7:120633600-120636600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr7:120633600-120636800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr7:120634000-120635200	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:120634000-120636200	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:120634000-120636400	Weak transcription	Stomach Mucosa	stomach
27	chr7:120634000-120637400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:120634200-120634800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:120634200-120634800	Active TSS	Stomach Smooth Muscle	stomach
30	chr7:120634200-120634800	Active TSS	NHLF	lung
31	chr7:120634200-120635000	Active TSS	Aorta	Aorta
32	chr7:120634200-120635000	Enhancers	Small Intestine	intestine
33	chr7:120634200-120635400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
34	chr7:120634200-120635600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:120634200-120635800	Strong transcription	HSMM	muscle
36	chr7:120634200-120636000	Weak transcription	Left Ventricle	heart
37	chr7:120634200-120636200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:120634200-120636200	Enhancers	Adipose Nuclei	Adipose
39	chr7:120634200-120636200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:120634200-120636200	Weak transcription	Fetal Lung	lung
41	chr7:120634200-120636200	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:120634200-120636200	Weak transcription	Psoas Muscle	Psoas
43	chr7:120634200-120636800	Weak transcription	NH-A	brain
44	chr7:120634200-120644000	Weak transcription	Spleen	Spleen
45	chr7:120634400-120634800	Weak transcription	Fetal Kidney	kidney
46	chr7:120634400-120634800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:120634600-120634800	Enhancers	Right Atrium	heart
48	chr7:120634600-120634800	Enhancers	Right Ventricle	heart
49	chr7:120634600-120635000	Enhancers	Fetal Heart	heart
50	chr7:120634600-120635000	Flanking Active TSS	Ovary	ovary

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