Variant report

Variant	rs41704
Chromosome Location	chr7:120644557-120644558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120579519..120582035-chr7:120642680..120645197,2	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: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10229719	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10258025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11363	0.83[EUR][1000 genomes]
rs12672149	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13881	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs193727	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2013083	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2013087	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs2074576	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs2074577	0.85[CEU][hapmap]
rs2215786	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2215789	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2244863	0.85[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525711	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2525714	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2525715	1.00[CEU][hapmap]
rs2525716	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525717	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525718	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525719	0.90[CEU][hapmap]
rs2525720	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525722	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525723	0.81[EUR][1000 genomes]
rs2525724	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525725	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2525726	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525728	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2525731	0.81[EUR][1000 genomes]
rs2525732	0.84[EUR][1000 genomes]
rs2525733	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2525734	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2525735	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs2525738	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs2525739	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2525740	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs2525741	0.81[EUR][1000 genomes]
rs2721350	1.00[CEU][hapmap]
rs2721351	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2721358	0.81[EUR][1000 genomes]
rs2721359	0.96[EUR][1000 genomes]
rs2721361	0.96[EUR][1000 genomes]
rs2721363	0.81[EUR][1000 genomes]
rs2721366	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2721368	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2721370	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2721372	0.90[CEU][hapmap]
rs2896299	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3944026	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41688	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs41689	0.81[EUR][1000 genomes]
rs41691	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]
rs41692	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41693	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41694	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41695	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41697	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727915	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4730985	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4730987	0.81[AMR][1000 genomes]
rs6966297	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6973457	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7789501	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7808535	0.84[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.85[EUR][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	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
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030988	chr7:120636796-120672504	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41704	KCND2	cis	cerebellum	SCAN
rs41704	SPAM1	cis	parietal	SCAN
rs41704	TSPAN12	cis	Artery Tibial	GTEx
rs41704	FLJ21986	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120637000-120646800	Weak transcription	Placenta	Placenta
2	chr7:120637200-120647000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:120637200-120663600	Weak transcription	Right Ventricle	heart
4	chr7:120639000-120645000	Enhancers	Liver	Liver
5	chr7:120640000-120644800	Enhancers	Fetal Stomach	stomach
6	chr7:120640400-120644800	Genic enhancers	HSMM	muscle
7	chr7:120640800-120646000	Weak transcription	Brain Anterior Caudate	brain
8	chr7:120642000-120645000	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr7:120642000-120647000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:120642200-120644800	Enhancers	Colon Smooth Muscle	Colon
11	chr7:120642400-120644600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr7:120642400-120644600	Enhancers	Rectal Smooth Muscle	rectum
13	chr7:120642600-120644800	Genic enhancers	K562	blood
14	chr7:120642600-120646400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr7:120642600-120646600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:120642800-120645800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:120643000-120644800	Enhancers	Ovary	ovary
18	chr7:120643200-120644600	Enhancers	Psoas Muscle	Psoas
19	chr7:120643200-120644800	Enhancers	Aorta	Aorta
20	chr7:120643200-120644800	Enhancers	Fetal Muscle Leg	muscle
21	chr7:120643200-120646000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:120643200-120646200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:120643200-120646600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:120643200-120646600	Weak transcription	Fetal Kidney	kidney
25	chr7:120643400-120644600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr7:120643400-120646000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:120643600-120644600	Enhancers	Right Atrium	heart
28	chr7:120643600-120644800	Enhancers	Left Ventricle	heart
29	chr7:120643600-120645800	Weak transcription	NHDF-Ad	bronchial
30	chr7:120643600-120646000	Weak transcription	Fetal Lung	lung
31	chr7:120643600-120646600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:120643600-120646800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:120643600-120646800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:120644000-120644600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:120644000-120644600	Enhancers	Spleen	Spleen
36	chr7:120644000-120646000	Weak transcription	Adipose Nuclei	Adipose
37	chr7:120644000-120646400	Weak transcription	NH-A	brain
38	chr7:120644200-120644600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:120644200-120644600	Weak transcription	Osteobl	bone
40	chr7:120644200-120646000	Weak transcription	NHLF	lung
41	chr7:120644400-120644600	Enhancers	Stomach Smooth Muscle	stomach
42	chr7:120644400-120644800	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr7:120644400-120644800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr7:120644400-120644800	Enhancers	HSMMtube	muscle

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