Variant report

Variant	rs35707546
Chromosome Location	chr17:45001541-45001542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr17:44999657-45002150	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr17:44999989-45001900	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45000610..45002133-chr17:45017223..45020134,3	MCF-7	breast:
2	chr17:44999992..45001971-chr17:45015932..45018557,3	MCF-7	breast:
3	chr17:44995313..44999079-chr17:44999263..45002356,3	MCF-7	breast:
4	chr17:45000734..45002965-chr17:45025082..45026604,2	K562	blood:
5	chr15:44089561..44091456-chr17:44999592..45001929,2	MCF-7	breast:
6	chr17:44974470..44976026-chr17:45001185..45003894,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261886	TF binding region
ENSG00000184716	Chromatin interaction
ENSG00000210709	Chromatin interaction
ENSG00000108433	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1047779	0.98[ASN][1000 genomes]
rs1052504	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1052586	0.97[ASN][1000 genomes]
rs10853085	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853086	0.89[EUR][1000 genomes]
rs10853087	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079744	0.85[EUR][1000 genomes]
rs11079745	0.96[ASN][1000 genomes]
rs11652318	0.96[ASN][1000 genomes]
rs11654971	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655668	0.87[EUR][1000 genomes]
rs11656362	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11658276	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11869840	0.98[ASN][1000 genomes]
rs12601886	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12940071	0.98[ASN][1000 genomes]
rs1618989	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1623402	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662576	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662577	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662594	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662596	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662597	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17608961	0.96[ASN][1000 genomes]
rs1838105	0.89[EUR][1000 genomes]
rs1867237	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197912	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs197913	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs197915	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs197917	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs197918	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197919	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197922	0.89[EUR][1000 genomes]
rs197923	0.89[EUR][1000 genomes]
rs197925	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs197926	0.96[ASN][1000 genomes]
rs2003538	0.94[ASN][1000 genomes]
rs2003539	0.98[ASN][1000 genomes]
rs2072317	0.85[EUR][1000 genomes]
rs2191033	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2316330	0.96[ASN][1000 genomes]
rs2317997	0.98[ASN][1000 genomes]
rs28553405	0.90[ASN][1000 genomes]
rs2920396	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920397	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3760377	0.96[ASN][1000 genomes]
rs3785888	0.98[ASN][1000 genomes]
rs3809854	0.96[ASN][1000 genomes]
rs3851784	0.96[ASN][1000 genomes]
rs3851785	0.96[ASN][1000 genomes]
rs3851786	0.92[ASN][1000 genomes]
rs3851787	0.94[ASN][1000 genomes]
rs3885731	0.84[EUR][1000 genomes]
rs3890958	0.84[EUR][1000 genomes]
rs4381655	0.96[ASN][1000 genomes]
rs4602097	0.96[ASN][1000 genomes]
rs4968248	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4968250	0.96[ASN][1000 genomes]
rs4968285	0.96[ASN][1000 genomes]
rs4968286	0.98[ASN][1000 genomes]
rs4968287	0.95[ASN][1000 genomes]
rs4968288	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968290	0.86[ASN][1000 genomes]
rs62075889	0.98[ASN][1000 genomes]
rs6504622	0.98[ASN][1000 genomes]
rs7213526	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7225428	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7342957	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs736603	0.95[ASN][1000 genomes]
rs736604	0.98[ASN][1000 genomes]
rs740617	0.98[ASN][1000 genomes]
rs8065527	0.83[EUR][1000 genomes]
rs9889741	0.98[ASN][1000 genomes]
rs9889762	0.96[ASN][1000 genomes]
rs9893713	0.85[ASN][1000 genomes]
rs9898981	0.98[ASN][1000 genomes]
rs9901977	0.85[ASN][1000 genomes]
rs9911967	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35707546	GOSR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:44999600-45001800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr17:44999600-45002000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:44999600-45002200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr17:44999800-45001600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr17:44999800-45001600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr17:44999800-45001600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr17:44999800-45001600	Active TSS	Fetal Kidney	kidney
8	chr17:44999800-45001600	Active TSS	Ovary	ovary
9	chr17:44999800-45001600	Active TSS	K562	blood
10	chr17:44999800-45001800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr17:44999800-45001800	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr17:44999800-45002000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr17:44999800-45002000	Active TSS	Fetal Intestine Small	intestine
14	chr17:44999800-45002200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:44999800-45002200	Active TSS	Fetal Intestine Large	intestine
16	chr17:44999800-45002200	Active TSS	Psoas Muscle	Psoas
17	chr17:44999800-45002200	Active TSS	GM12878-XiMat	blood
18	chr17:45000000-45001600	Active TSS	Aorta	Aorta
19	chr17:45000000-45002000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:45000600-45001800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:45000800-45001600	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr17:45000800-45001600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr17:45000800-45001600	Flanking Active TSS	Fetal Brain Female	brain
24	chr17:45000800-45001600	Active TSS	Right Atrium	heart
25	chr17:45000800-45001800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr17:45000800-45002000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr17:45000800-45002200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr17:45001000-45001600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr17:45001000-45001600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr17:45001000-45001600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:45001000-45001600	Flanking Active TSS	Fetal Lung	lung
32	chr17:45001000-45001600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr17:45001000-45001800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:45001000-45001800	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr17:45001000-45001800	Weak transcription	Small Intestine	intestine
36	chr17:45001000-45002000	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr17:45001000-45002200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr17:45001000-45002400	Flanking Active TSS	Liver	Liver
39	chr17:45001200-45001600	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr17:45001200-45001600	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr17:45001200-45001600	Flanking Active TSS	Fetal Stomach	stomach
42	chr17:45001200-45001800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:45001200-45001800	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr17:45001200-45001800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr17:45001200-45001800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr17:45001200-45001800	Flanking Active TSS	NH-A	brain
47	chr17:45001200-45002000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr17:45001200-45002000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr17:45001200-45002000	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr17:45001200-45002000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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