Variant report

Variant	rs2955371
Chromosome Location	chr17:17967397-17967398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17967072..17969042-chr17:17971389..17973422,2	K562	blood:
2	chr17:17739170..17740871-chr17:17964937..17967522,2	MCF-7	breast:
3	chr17:17965517..17967965-chr17:17969575..17972463,2	MCF-7	breast:
4	chr17:17959821..17961989-chr17:17966641..17969324,2	K562	blood:

Variant related genes	Relation type
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10048206	0.91[CEU][hapmap]
rs11078406	0.91[CEU][hapmap]
rs11650021	0.81[EUR][1000 genomes]
rs11650649	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs11652894	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656840	0.91[CEU][hapmap]
rs12600546	0.91[CEU][hapmap]
rs12939020	0.81[EUR][1000 genomes]
rs12943202	0.87[ASN][1000 genomes]
rs12943500	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12943914	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12948749	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952818	0.87[ASN][1000 genomes]
rs2230316	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2350977	0.91[CEU][hapmap]
rs2955350	0.82[EUR][1000 genomes]
rs2955351	0.87[ASN][1000 genomes]
rs2955353	0.82[EUR][1000 genomes]
rs2955354	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2955355	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955356	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955357	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955358	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955359	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2955360	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955368	0.84[EUR][1000 genomes]
rs2955370	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2955372	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955378	0.81[CEU][hapmap]
rs2955380	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2955381	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2955382	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955383	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2955384	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2955385	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4077828	0.91[CEU][hapmap]
rs4244602	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs4257260	0.91[CEU][hapmap]
rs4321247	0.91[ASN][1000 genomes]
rs4341796	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs4368210	0.81[CEU][hapmap]
rs4413022	0.91[CEU][hapmap]
rs4459604	0.81[CEU][hapmap]
rs4470201	0.91[CEU][hapmap]
rs4584886	0.81[CEU][hapmap]
rs4643387	0.81[EUR][1000 genomes]
rs4924832	0.81[CEU][hapmap]
rs4925123	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs4925125	0.87[CEU][hapmap]
rs4925126	0.91[CEU][hapmap]
rs4925129	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs4925130	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs4925135	0.83[EUR][1000 genomes]
rs4925136	0.82[EUR][1000 genomes]
rs4925138	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5002487	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs62072049	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6502619	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs6502622	0.91[CEU][hapmap]
rs6502624	0.91[CEU][hapmap]
rs6502625	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs6502627	0.91[CEU][hapmap]
rs6502629	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs6502632	0.81[CEU][hapmap]
rs6502633	0.82[EUR][1000 genomes]
rs6502636	0.80[CEU][hapmap]
rs712265	0.87[ASN][1000 genomes]
rs7207395	0.82[JPT][hapmap]
rs7207461	0.82[EUR][1000 genomes]
rs7207821	0.82[CEU][hapmap]
rs7209003	0.82[CEU][hapmap]
rs7210400	0.83[EUR][1000 genomes]
rs7212167	0.81[CEU][hapmap]
rs7213225	0.91[CEU][hapmap]
rs7214002	0.91[CEU][hapmap]
rs7222480	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs7224815	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs72827413	0.87[ASN][1000 genomes]
rs7406982	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs7503334	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs7503738	0.80[EUR][1000 genomes]
rs8065416	0.91[CEU][hapmap]
rs8065563	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs8066982	0.91[CEU][hapmap]
rs8070128	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs8070748	0.91[CEU][hapmap]
rs8073001	0.91[CEU][hapmap]
rs8075189	0.81[CEU][hapmap]
rs8078105	0.90[CEU][hapmap]
rs8078138	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs8078583	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs8079418	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8080061	1.00[CEU][hapmap]
rs8080602	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs8080823	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs854762	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs854764	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs854765	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs854766	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs854810	0.87[ASN][1000 genomes]
rs854813	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs950966	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs9890341	0.91[CEU][hapmap]
rs9894138	0.83[EUR][1000 genomes]
rs9896837	0.81[CEU][hapmap]
rs9897761	0.82[CEU][hapmap]
rs9907246	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs9907287	1.00[CEU][hapmap]
rs9912895	0.91[CEU][hapmap]
rs9913277	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats 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 miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2955371	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17944000-17974200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:17944000-17974200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:17944200-17974400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:17944400-17978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:17947000-17974400	Weak transcription	Fetal Heart	heart
6	chr17:17950000-17974400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:17950800-17974000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr17:17953400-17970000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:17954000-17968600	Weak transcription	Psoas Muscle	Psoas
10	chr17:17954200-17974200	Weak transcription	Fetal Brain Male	brain
11	chr17:17954800-17974200	Weak transcription	Stomach Mucosa	stomach
12	chr17:17955600-17969400	Strong transcription	Fetal Muscle Leg	muscle
13	chr17:17955600-17969800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr17:17955600-17970600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr17:17955600-17971200	Strong transcription	Liver	Liver
16	chr17:17956600-17970800	Strong transcription	Fetal Intestine Small	intestine
17	chr17:17956800-17969400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:17956800-17969800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:17956800-17969800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:17957000-17970200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:17957200-17970600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr17:17957200-17970800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr17:17957400-17969400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr17:17960000-17969600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr17:17960400-17968600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr17:17961400-17969200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr17:17961400-17969200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:17961400-17969200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:17961400-17969400	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr17:17961400-17970400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr17:17961400-17970800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr17:17961400-17971200	Strong transcription	Fetal Intestine Large	intestine
33	chr17:17961400-17971200	Strong transcription	Fetal Stomach	stomach
34	chr17:17961600-17970600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr17:17961800-17969800	Strong transcription	Ovary	ovary
36	chr17:17961800-17970000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr17:17961800-17970800	Strong transcription	Placenta	Placenta
38	chr17:17962000-17969800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:17962200-17974200	Weak transcription	Fetal Kidney	kidney
40	chr17:17962600-17974200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr17:17962800-17967400	Weak transcription	Pancreas	Pancrea
42	chr17:17962800-17967400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr17:17962800-17968200	Weak transcription	A549	lung
44	chr17:17963000-17968400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:17963000-17970800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:17963000-17974200	Weak transcription	HUVEC	blood vessel
47	chr17:17963400-17971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:17963800-17971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:17963800-17971400	Strong transcription	Brain Anterior Caudate	brain
50	chr17:17964000-17970000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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