Variant report

Variant	rs4246073
Chromosome Location	chr6:5214983-5214984
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5214686..5215658-chr6:5401229..5403280,10	K562	blood:
2	chr6:5214761..5215392-chr6:5379547..5380560,3	MCF-7	breast:
3	chr6:5209168..5211266-chr6:5213691..5215244,2	K562	blood:
4	chr6:5214746..5216032-chr6:5379652..5380557,3	K562	blood:
5	chr6:5214762..5218085-chr6:5221984..5224598,3	K562	blood:
6	chr6:5214744..5215638-chr6:5398420..5399368,7	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1055415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12206736	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535041	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1570085	1.00[JPT][hapmap]
rs17139748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884976	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1970010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2145372	1.00[JPT][hapmap]
rs2224391	1.00[JPT][hapmap]
rs2746220	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2746221	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2746222	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746224	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2746226	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2746243	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2753214	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2753230	1.00[JPT][hapmap]
rs2753235	1.00[JPT][hapmap]
rs2753237	1.00[JPT][hapmap]
rs2753238	1.00[JPT][hapmap]
rs2753239	1.00[JPT][hapmap]
rs2753244	1.00[JPT][hapmap]
rs2753245	1.00[JPT][hapmap]
rs2753246	1.00[JPT][hapmap]
rs2753248	1.00[JPT][hapmap]
rs2753255	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2773287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2773289	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2773291	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2773294	0.95[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2773296	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2773311	1.00[JPT][hapmap]
rs2773314	1.00[JPT][hapmap]
rs2773316	1.00[JPT][hapmap]
rs2773317	1.00[JPT][hapmap]
rs2773318	1.00[JPT][hapmap]
rs2773319	1.00[JPT][hapmap]
rs2773333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2773335	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2773336	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2773337	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2773339	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35943326	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367803	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs374253	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs391313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs393391	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs393454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs399283	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs409295	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs416803	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs421186	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs421720	0.95[CEU][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs429031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs434450	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs439356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs445711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs447604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4960073	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4960074	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs761359	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761360	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9328289	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9378943	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9392664	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9392665	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9405807	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs9405809	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9504356	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9504370	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking 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 miRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	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
rs4246073	FARS2	cis	lymphoblastoid	seeQTL
rs4246073	LYRM4	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5176200-5239600	Weak transcription	Thymus	Thymus
2	chr6:5194000-5220800	Weak transcription	GM12878-XiMat	blood
3	chr6:5205600-5218800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:5205600-5220000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:5205600-5223000	Weak transcription	Right Atrium	heart
6	chr6:5206200-5215600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:5206200-5215600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:5206200-5246800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:5206400-5219400	Weak transcription	HMEC	breast
10	chr6:5206600-5215800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:5206600-5216200	Weak transcription	Pancreas	Pancrea
12	chr6:5206600-5240800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:5206800-5215000	Weak transcription	HUVEC	blood vessel
14	chr6:5206800-5217400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:5206800-5221000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:5206800-5232400	Weak transcription	Psoas Muscle	Psoas
17	chr6:5207000-5231000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:5207600-5216400	Strong transcription	HepG2	liver
19	chr6:5208200-5259800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:5208400-5231400	Weak transcription	Brain Anterior Caudate	brain
21	chr6:5208400-5239800	Weak transcription	Liver	Liver
22	chr6:5208600-5216000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:5208800-5231000	Weak transcription	Brain Angular Gyrus	brain
24	chr6:5210000-5230400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:5211600-5215400	Strong transcription	K562	blood
26	chr6:5211800-5215600	Enhancers	Fetal Heart	heart
27	chr6:5212200-5215200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:5212400-5215000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:5212400-5215600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr6:5212400-5217000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:5212600-5215000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:5212600-5215200	Strong transcription	Adipose Nuclei	Adipose
33	chr6:5212600-5218200	Strong transcription	Primary T cells from cord blood	blood
34	chr6:5212600-5230800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:5212800-5216200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:5213000-5215400	Strong transcription	Hela-S3	cervix
37	chr6:5213000-5215600	Strong transcription	Primary B cells from cord blood	blood
38	chr6:5213000-5216800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:5213200-5215200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:5213200-5215200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:5213400-5215000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr6:5213400-5215400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:5213400-5216200	Strong transcription	Fetal Brain Female	brain
44	chr6:5213400-5216400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:5213600-5215000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:5213600-5215000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:5213600-5215000	Strong transcription	Gastric	stomach
48	chr6:5213600-5215200	Strong transcription	NHEK	skin
49	chr6:5213600-5215400	Strong transcription	Dnd41	blood
50	chr6:5213600-5216400	Strong transcription	Skeletal Muscle Male	skeletal muscle

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