Variant report

Variant	rs740160
Chromosome Location	chr7:98957880-98957881
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	chr7:98957301..98959379-chr7:98970732..98973390,3	MCF-7	breast:
2	chr7:98953069..98956142-chr7:98957190..98959083,3	K562	blood:

Variant related genes	Relation type
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10215765	1.00[ASN][1000 genomes]
rs10215854	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10226310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10229886	1.00[ASN][1000 genomes]
rs10230784	1.00[ASN][1000 genomes]
rs10235235	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10236240	1.00[ASN][1000 genomes]
rs10264505	1.00[ASN][1000 genomes]
rs10268984	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs10275381	1.00[ASN][1000 genomes]
rs10277447	1.00[ASN][1000 genomes]
rs10808111	1.00[CHB][hapmap]
rs10808112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10953288	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs10953289	1.00[ASN][1000 genomes]
rs11555142	1.00[ASN][1000 genomes]
rs11761528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11766423	1.00[ASN][1000 genomes]
rs11971640	1.00[ASN][1000 genomes]
rs11972017	1.00[CHB][hapmap]
rs11973173	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11973801	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11974593	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11974885	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11977673	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs11978345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980143	1.00[ASN][1000 genomes]
rs11980995	1.00[ASN][1000 genomes]
rs11980999	1.00[ASN][1000 genomes]
rs11983474	1.00[ASN][1000 genomes]
rs12531852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12533251	1.00[ASN][1000 genomes]
rs12535424	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12536002	1.00[ASN][1000 genomes]
rs12539480	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223272	1.00[ASN][1000 genomes]
rs13227522	1.00[ASN][1000 genomes]
rs13243267	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17161687	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161761	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2003498	1.00[ASN][1000 genomes]
rs2395048	0.82[CEU][hapmap]
rs28419687	1.00[ASN][1000 genomes]
rs28602855	1.00[ASN][1000 genomes]
rs28627543	1.00[ASN][1000 genomes]
rs34111611	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34257469	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs35183025	1.00[ASN][1000 genomes]
rs35296070	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs35656351	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36104094	1.00[ASN][1000 genomes]
rs45618033	1.00[ASN][1000 genomes]
rs4765	1.00[ASN][1000 genomes]
rs55761861	1.00[ASN][1000 genomes]
rs56937678	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57786744	1.00[ASN][1000 genomes]
rs57980352	1.00[ASN][1000 genomes]
rs58964157	1.00[ASN][1000 genomes]
rs60127638	1.00[ASN][1000 genomes]
rs60577432	1.00[ASN][1000 genomes]
rs61740607	1.00[ASN][1000 genomes]
rs66478766	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66509940	1.00[ASN][1000 genomes]
rs66568021	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66674233	1.00[ASN][1000 genomes]
rs67279166	1.00[ASN][1000 genomes]
rs67309224	1.00[ASN][1000 genomes]
rs67546174	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67860332	1.00[ASN][1000 genomes]
rs67909852	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67934834	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947826	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6947941	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6947974	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6955891	1.00[ASN][1000 genomes]
rs6960805	1.00[CHB][hapmap]
rs6960810	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs6961579	1.00[CHB][hapmap]
rs6964049	1.00[EUR][1000 genomes]
rs704798	1.00[ASN][1000 genomes]
rs73157587	1.00[ASN][1000 genomes]
rs73157588	1.00[ASN][1000 genomes]
rs73157589	1.00[ASN][1000 genomes]
rs73157590	1.00[ASN][1000 genomes]
rs73157596	1.00[ASN][1000 genomes]
rs73157600	1.00[ASN][1000 genomes]
rs73157601	1.00[ASN][1000 genomes]
rs73157602	1.00[ASN][1000 genomes]
rs73159506	1.00[ASN][1000 genomes]
rs73159509	1.00[ASN][1000 genomes]
rs73159522	1.00[ASN][1000 genomes]
rs73163167	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73163169	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7778859	1.00[ASN][1000 genomes]
rs868391	1.00[ASN][1000 genomes]
rs9632722	1.00[ASN][1000 genomes]
rs9656060	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Dehydroepiandrosterone sulphate levels	21533175	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs740160	ARPC1B	cis	Thyroid	GTEx
rs740160	GS1-259H13.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98924600-98971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:98925200-98965200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:98927200-98966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:98927800-98960600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:98928400-98967200	Strong transcription	Fetal Thymus	thymus
6	chr7:98928600-98965200	Strong transcription	Dnd41	blood
7	chr7:98929000-98965600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:98929400-98965200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:98929600-98962800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr7:98929600-98965400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr7:98929800-98965000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr7:98930000-98962800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:98930000-98968200	Strong transcription	Fetal Intestine Small	intestine
14	chr7:98930200-98968400	Strong transcription	Fetal Stomach	stomach
15	chr7:98930600-98965200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr7:98930600-98965200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:98930600-98965200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:98930800-98960200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:98930800-98965200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:98930800-98965200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:98930800-98965400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr7:98930800-98966800	Strong transcription	Adipose Nuclei	Adipose
23	chr7:98930800-98967000	Strong transcription	Fetal Muscle Leg	muscle
24	chr7:98930800-98967600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr7:98931000-98959600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:98931000-98960200	Strong transcription	Placenta	Placenta
27	chr7:98931000-98965000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:98932600-98966400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:98934400-98965200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr7:98935600-98971600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr7:98939600-98965400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:98939800-98965200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:98939800-98965200	Strong transcription	Fetal Intestine Large	intestine
34	chr7:98940200-98965000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:98940600-98965000	Strong transcription	Primary T cells from cord blood	blood
36	chr7:98941200-98959800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:98941200-98963000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:98941600-98965200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr7:98944200-98967200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr7:98944400-98959200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:98944400-98965200	Strong transcription	Thymus	Thymus
42	chr7:98944400-98965400	Strong transcription	Spleen	Spleen
43	chr7:98944600-98965200	Strong transcription	Lung	lung
44	chr7:98945600-98963200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:98945600-98963200	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr7:98946400-98967600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr7:98947600-98960200	Strong transcription	Osteobl	bone
48	chr7:98948200-98960200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:98951000-98965000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr7:98951000-98967000	Strong transcription	Left Ventricle	heart

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