Variant report

Variant	rs6544214
Chromosome Location	chr2:39477170-39477171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39476438..39480963-chr2:39481034..39484561,4	K562	blood:
2	chr2:39476355..39478295-chr2:39480403..39482715,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1012689	0.87[ASN][1000 genomes]
rs10175094	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10185961	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10193807	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10196407	0.84[CHB][hapmap]
rs10865148	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11124667	0.86[ASN][1000 genomes]
rs11124671	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11124675	0.93[CHB][hapmap]
rs11124680	0.84[CHB][hapmap]
rs11677383	1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12151392	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12162306	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12617901	1.00[CHB][hapmap];0.82[TSI][hapmap]
rs12618944	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12624242	0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12712634	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712640	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs12997072	0.87[EUR][1000 genomes]
rs13015356	0.82[ASN][1000 genomes]
rs13405577	0.85[EUR][1000 genomes]
rs1861733	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1861734	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2024514	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2302749	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2373528	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2888593	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755171	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755172	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755176	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770662	0.86[CHB][hapmap]
rs3770664	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs3770671	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770672	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770673	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770674	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4488638	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62138511	0.82[ASN][1000 genomes]
rs6544215	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544216	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6709424	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs6714566	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6719469	0.83[EUR][1000 genomes]
rs6743345	0.84[CHB][hapmap]
rs6753014	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7340455	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs7561630	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7569037	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7569492	0.87[EUR][1000 genomes]
rs7573923	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7581692	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7582848	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7594145	0.84[ASN][1000 genomes]
rs7595469	0.87[EUR][1000 genomes]
rs7597300	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7598583	0.80[CHD][hapmap]
rs7608958	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9037	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309036	0.90[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs9309037	0.80[CHB][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	36 gene(s)	inside rSNPs	diseases
5	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv2693	chr2:39468641-39513800	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv873886	chr2:39468676-39573521	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	esv1809158	chr2:39474679-39588797	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544214	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39449200-39477600	Weak transcription	HSMMtube	muscle
2	chr2:39469200-39477400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:39469200-39478000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:39469200-39503800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:39469400-39477600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:39469400-39504200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:39469600-39477600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:39469600-39478000	Weak transcription	Gastric	stomach
9	chr2:39471000-39477600	Weak transcription	Fetal Kidney	kidney
10	chr2:39471000-39477800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:39471000-39503400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:39471200-39477200	Weak transcription	Liver	Liver
13	chr2:39471200-39477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:39471200-39477600	Weak transcription	Brain Anterior Caudate	brain
15	chr2:39471200-39477600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:39471200-39477600	Weak transcription	Fetal Lung	lung
17	chr2:39471200-39477600	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:39471200-39477600	Weak transcription	GM12878-XiMat	blood
19	chr2:39471200-39477600	Weak transcription	HUVEC	blood vessel
20	chr2:39471200-39477600	Weak transcription	NHLF	lung
21	chr2:39471200-39477600	Weak transcription	Osteobl	bone
22	chr2:39471200-39477800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:39471200-39478000	Weak transcription	Left Ventricle	heart
24	chr2:39471200-39478200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:39471200-39478600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:39471200-39479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:39471200-39479400	Weak transcription	Lung	lung
28	chr2:39471200-39480000	Weak transcription	Pancreas	Pancrea
29	chr2:39471200-39480200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:39471200-39483800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:39471200-39503800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:39471200-39504200	Weak transcription	Esophagus	oesophagus
33	chr2:39471400-39477200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:39471400-39477400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:39471400-39477600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:39471400-39477600	Weak transcription	Colonic Mucosa	Colon
37	chr2:39471400-39477600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:39471400-39477600	Weak transcription	Ovary	ovary
39	chr2:39471400-39477800	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:39471400-39477800	Weak transcription	Fetal Brain Female	brain
41	chr2:39471400-39477800	Weak transcription	Fetal Stomach	stomach
42	chr2:39471400-39503400	Weak transcription	Right Ventricle	heart
43	chr2:39471600-39477600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:39471600-39478000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:39471800-39477600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:39471800-39477800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:39471800-39480400	Weak transcription	Spleen	Spleen
48	chr2:39472000-39477400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:39472000-39477800	Weak transcription	Fetal Intestine Large	intestine
50	chr2:39472600-39477600	Weak transcription	Rectal Mucosa Donor 29	rectum

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