Variant report

Variant	rs2505671
Chromosome Location	chr6:2357643-2357644
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:2207154..2208883-chr6:2356432..2359117,2	K562	blood:
2	chr6:2357336..2360924-chr6:2363674..2365844,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRNIP1-35	chr6:2356966-2362624	NONHSAT106650

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11242758	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962550	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11963138	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11963529	0.81[ASN][1000 genomes]
rs12191002	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661136	0.93[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs13196306	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13217030	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2295008	0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2450299	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450304	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2450307	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450310	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2479001	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479002	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479004	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479008	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479011	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479014	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505657	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505658	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505659	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505660	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505661	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505662	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505663	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505666	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505667	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2505670	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505673	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505677	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505678	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3778568	0.92[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs3800184	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs3800185	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs3800187	0.81[ASN][1000 genomes]
rs3800190	0.93[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3823287	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs55992523	0.80[ASN][1000 genomes]
rs56196406	0.81[ASN][1000 genomes]
rs6596879	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936538	0.83[AFR][1000 genomes]
rs72830184	0.81[ASN][1000 genomes]
rs7754950	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9328087	0.88[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378686	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs9378687	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs9378688	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9378692	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378693	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9391946	0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9392374	0.92[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9392375	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9392377	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9405550	0.92[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9766688	0.83[AFR][1000 genomes]
rs9766689	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2505671	LOC728772///TMEM106A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2339200-2370000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:2344400-2377400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:2345400-2365800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:2347000-2362800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:2349400-2362000	Weak transcription	Spleen	Spleen
6	chr6:2352000-2362400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:2352400-2376400	Weak transcription	HSMMtube	muscle
8	chr6:2352800-2360200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:2353800-2376400	Weak transcription	Pancreas	Pancrea
10	chr6:2354200-2360000	Weak transcription	Fetal Intestine Small	intestine
11	chr6:2354200-2360200	Weak transcription	Fetal Stomach	stomach
12	chr6:2354200-2360400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:2354200-2360800	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:2354200-2362200	Weak transcription	Ovary	ovary
15	chr6:2354200-2363200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:2354200-2363200	Weak transcription	Adipose Nuclei	Adipose
17	chr6:2354200-2366800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:2354200-2367200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:2354200-2371600	Weak transcription	Right Ventricle	heart
20	chr6:2354200-2376400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:2354400-2361000	Weak transcription	Fetal Intestine Large	intestine
22	chr6:2354600-2361800	Weak transcription	Liver	Liver
23	chr6:2356000-2363400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:2356200-2362800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:2356200-2369800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:2356200-2382200	Weak transcription	Aorta	Aorta
27	chr6:2356600-2382800	Weak transcription	Psoas Muscle	Psoas
28	chr6:2356800-2363400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:2357000-2363800	Weak transcription	Brain Anterior Caudate	brain
30	chr6:2357200-2359800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:2357400-2363400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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