Variant report

Variant	rs7538853
Chromosome Location	chr1:212926426-212926427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212924762..212928442-chr1:212932501..212935953,4	K562	blood:
2	chr1:212926276..212926792-chr1:213168366..213168980,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10127613	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1032963	0.85[EUR][1000 genomes]
rs1032964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779583	0.92[EUR][1000 genomes]
rs10863992	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10864002	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs10864003	0.82[YRI][hapmap]
rs11120005	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11120034	0.91[EUR][1000 genomes]
rs11120038	0.86[EUR][1000 genomes]
rs12133194	0.87[EUR][1000 genomes]
rs12239017	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12568552	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12744555	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs12757944	0.91[EUR][1000 genomes]
rs1507359	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1580991	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1580992	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1605420	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1813705	0.93[EUR][1000 genomes]
rs1848243	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292214	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884675	0.91[EUR][1000 genomes]
rs3738802	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3949369	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs4520475	0.81[ASN][1000 genomes]
rs4639827	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951639	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6540766	0.93[EUR][1000 genomes]
rs6540767	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs6665489	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6670373	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6670869	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678961	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6681851	0.87[EUR][1000 genomes]
rs6685864	0.87[EUR][1000 genomes]
rs6686145	0.86[EUR][1000 genomes]
rs6686164	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689799	0.86[EUR][1000 genomes]
rs6694887	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696870	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs6696908	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700465	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6702544	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6703982	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7513199	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513210	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513734	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513772	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7514070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7522100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528303	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs7535608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7543603	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7547100	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7555930	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking 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	33 gene(s)	inside rSNPs	diseases
5	nsv1005983	chr1:212917531-212947521	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv159271	chr1:212926246-212928111	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7538853	SNFT	cis	multi-tissue	Pritchard
rs7538853	FLVCR1-AS1	cis	Whole Blood	GTEx
rs7538853	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs7538853	NSL1	cis	Lymphoblastoid	GTEx
rs7538853	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs7538853	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs7538853	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs7538853	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212898800-212934000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:212900400-212927600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:212900400-212932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:212900400-212936200	Weak transcription	Aorta	Aorta
7	chr1:212901400-212954000	Weak transcription	NH-A	brain
8	chr1:212902200-212941800	Weak transcription	Fetal Kidney	kidney
9	chr1:212902600-212943600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:212908000-212933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:212912000-212935800	Weak transcription	K562	blood
12	chr1:212915400-212932600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:212915400-212933400	Weak transcription	Ovary	ovary
14	chr1:212915400-212934400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:212915400-212936000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:212915400-212942000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:212917600-212931200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:212918400-212929400	Weak transcription	Fetal Stomach	stomach
19	chr1:212918800-212930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:212920000-212929200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:212920600-212929400	Weak transcription	Fetal Intestine Small	intestine
22	chr1:212921000-212929400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:212922200-212939600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:212923400-212928600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:212923600-212927600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:212923600-212927800	Weak transcription	Left Ventricle	heart
27	chr1:212923600-212932800	Weak transcription	Fetal Intestine Large	intestine
28	chr1:212923600-212935400	Weak transcription	Lung	lung
29	chr1:212923600-212956200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
31	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:212923800-212926600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:212923800-212926600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:212923800-212927200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:212923800-212927200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:212923800-212927400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:212923800-212927400	Enhancers	Primary T cells from cord blood	blood
38	chr1:212923800-212928000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:212923800-212931000	Weak transcription	Dnd41	blood
40	chr1:212923800-212932600	Weak transcription	Spleen	Spleen
41	chr1:212923800-212935800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:212923800-212935800	Weak transcription	Placenta	Placenta
43	chr1:212923800-212947200	Weak transcription	A549	lung
44	chr1:212923800-212957600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:212923800-212964200	Weak transcription	HMEC	breast
46	chr1:212924000-212927000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:212924000-212928200	Weak transcription	Right Ventricle	heart
48	chr1:212924000-212930000	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:212924000-212930200	Weak transcription	HepG2	liver
50	chr1:212924000-212954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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