Variant report

Variant	rs11978345
Chromosome Location	chr7:98930036-98930037
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:98915839..98918656-chr7:98927635..98930198,2	MCF-7	breast:
2	chr7:98921268..98926325-chr7:98927709..98931236,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241685	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

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];0.90[AMR][1000 genomes];0.93[EUR][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];0.84[AFR][1000 genomes];0.95[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[AMR][1000 genomes];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];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161761	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[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]
rs45618033	1.00[ASN][1000 genomes]
rs4765	1.00[ASN][1000 genomes]
rs55761861	1.00[ASN][1000 genomes]
rs56937678	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	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66509940	1.00[ASN][1000 genomes]
rs66568021	0.85[AFR][1000 genomes];0.95[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	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67860332	1.00[ASN][1000 genomes]
rs67909852	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67934834	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947826	1.00[ASN][1000 genomes]
rs6947941	1.00[ASN][1000 genomes]
rs6947974	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[AMR][1000 genomes];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]
rs740160	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]
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:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11978345	ARPC1B	cis	Thyroid	GTEx
rs11978345	GS1-259H13.2	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98924400-98957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:98924600-98930200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr7:98924600-98971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:98924800-98930800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:98924800-98930800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:98924800-98930800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:98924800-98930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:98924800-98930800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:98924800-98931000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:98924800-98931000	Weak transcription	Fetal Kidney	kidney
11	chr7:98924800-98932600	Weak transcription	Aorta	Aorta
12	chr7:98924800-98935600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:98924800-98935600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:98924800-98935800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:98924800-98936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:98925000-98931000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:98925200-98930800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:98925200-98965200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:98925400-98935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:98925600-98930200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:98925600-98931000	Weak transcription	Thymus	Thymus
22	chr7:98925600-98931200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr7:98925600-98936200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:98925800-98930800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr7:98925800-98930800	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:98925800-98930800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:98925800-98931200	Weak transcription	Gastric	stomach
28	chr7:98925800-98933600	Weak transcription	Colonic Mucosa	Colon
29	chr7:98926000-98931000	Weak transcription	Fetal Brain Male	brain
30	chr7:98926200-98930800	Weak transcription	Liver	Liver
31	chr7:98926200-98931200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:98926200-98934200	Weak transcription	Spleen	Spleen
33	chr7:98926400-98930600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:98926400-98930800	Weak transcription	Adipose Nuclei	Adipose
35	chr7:98926400-98931000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:98926400-98931200	Weak transcription	Ovary	ovary
37	chr7:98926400-98933000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr7:98926400-98935600	Weak transcription	Brain Substantia Nigra	brain
39	chr7:98926400-98935800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr7:98926600-98930200	Weak transcription	Fetal Stomach	stomach
41	chr7:98926600-98930800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr7:98926600-98931200	Weak transcription	Lung	lung
43	chr7:98926600-98932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:98926600-98941600	Weak transcription	Psoas Muscle	Psoas
45	chr7:98927200-98931000	Weak transcription	Brain Anterior Caudate	brain
46	chr7:98927200-98966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:98927400-98930600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:98927400-98930800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr7:98927400-98930800	Weak transcription	Fetal Brain Female	brain
50	chr7:98927400-98931000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links