Variant report

Variant	rs55955603
Chromosome Location	chr1:161295245-161295246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161295193-161295436	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161283899..161285656-chr1:161294707..161297555,2	MCF-7	breast:

Variant related genes	Relation type
SDHC	TF binding region
ENSG00000143252	Chromatin interaction

Extended variants
information (count: 166 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:163)

rs_ID	r²[population]
rs10158388	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10159083	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10494350	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10494351	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10494352	0.83[ASN][1000 genomes]
rs10494353	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10494354	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1133805	0.83[ASN][1000 genomes]
rs1133806	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11588994	0.81[ASN][1000 genomes]
rs12239492	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12239719	0.83[ASN][1000 genomes]
rs12385723	0.82[AFR][1000 genomes]
rs12385733	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12725465	0.81[ASN][1000 genomes]
rs12730813	0.80[ASN][1000 genomes]
rs12738660	0.81[ASN][1000 genomes]
rs12745476	0.80[ASN][1000 genomes]
rs13374037	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13375385	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13376158	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832811	0.84[AFR][1000 genomes]
rs16832813	0.84[AFR][1000 genomes]
rs16832817	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs16832820	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs16832823	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs16832824	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832826	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs16832835	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832842	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832846	0.83[ASN][1000 genomes]
rs16832851	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832854	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832869	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832871	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832874	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832883	0.84[ASN][1000 genomes]
rs16832884	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832887	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832892	0.82[ASN][1000 genomes]
rs16832894	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832897	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832900	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832902	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16832908	0.83[ASN][1000 genomes]
rs16832922	0.83[ASN][1000 genomes]
rs3087596	0.83[ASN][1000 genomes]
rs34872203	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35006684	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35680024	0.84[ASN][1000 genomes]
rs3934593	0.81[ASN][1000 genomes]
rs3935401	0.83[ASN][1000 genomes]
rs4077289	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4077290	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4077631	0.84[ASN][1000 genomes]
rs41270861	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4255402	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4291521	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4319356	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4360541	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4463689	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4469725	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4474277	0.82[AFR][1000 genomes]
rs4477296	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4481873	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4525064	0.83[ASN][1000 genomes]
rs4534403	0.80[ASN][1000 genomes]
rs4534404	0.83[ASN][1000 genomes]
rs4534405	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4585997	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4600063	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4622080	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4631719	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4634926	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4634927	0.80[ASN][1000 genomes]
rs55674249	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs55682614	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55698724	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs55729989	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs55747162	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs55783815	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs55807618	0.83[ASN][1000 genomes]
rs55809622	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs55898518	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55929617	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs55961103	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55962831	0.83[ASN][1000 genomes]
rs55981028	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs55996762	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs56007456	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs56028608	0.82[ASN][1000 genomes]
rs56062031	0.84[ASN][1000 genomes]
rs56071922	0.82[AFR][1000 genomes]
rs56122953	0.84[ASN][1000 genomes]
rs56169917	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs56269923	0.84[AFR][1000 genomes]
rs56280055	0.86[AFR][1000 genomes]
rs56290916	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs56355322	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs56406825	0.83[ASN][1000 genomes]
rs56411570	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs56868836	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57007882	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57154376	0.82[ASN][1000 genomes]
rs57270150	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57306652	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57421557	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57473118	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57474688	0.84[ASN][1000 genomes]
rs57835711	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57841279	0.83[ASN][1000 genomes]
rs57858140	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58138146	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58418155	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs58758353	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58842513	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58874147	0.83[ASN][1000 genomes]
rs59037769	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs59191996	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59340690	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59544428	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59559479	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59690240	0.84[AFR][1000 genomes]
rs59747425	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59774375	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59840298	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs60078979	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs60179510	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs60261157	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs60345130	0.84[ASN][1000 genomes]
rs60382588	0.83[ASN][1000 genomes]
rs60405593	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs60435895	0.88[AFR][1000 genomes]
rs60792683	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs60799370	0.86[AFR][1000 genomes]
rs60882053	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61181161	0.82[ASN][1000 genomes]
rs61219424	0.84[ASN][1000 genomes]
rs61299084	0.83[ASN][1000 genomes]
rs61304797	0.86[AFR][1000 genomes]
rs61308286	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs61447446	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs61461118	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs61576374	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs61618989	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs61653684	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6675552	0.81[ASN][1000 genomes]
rs6688180	0.81[ASN][1000 genomes]
rs7412460	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs74124931	0.84[ASN][1000 genomes]
rs74127622	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs74127629	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs74127630	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs74127635	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs74127636	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs74127638	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs74127639	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs74127641	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs74127657	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs74127658	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7542784	0.80[ASN][1000 genomes]
rs9330294	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9970904	0.86[AFR][1000 genomes];0.83[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	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1010776	chr1:161282384-161409218	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv3350144	chr1:161293402-161298235	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs55955603	RP11-122G18.5	cis	Artery Tibial	GTEx
rs55955603	SDHC	Cis_1M	lymphoblastoid	RTeQTL
rs55955603	SDHC	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161284800-161300400	Weak transcription	Aorta	Aorta
2	chr1:161285000-161295600	Weak transcription	Gastric	stomach
3	chr1:161285000-161296600	Weak transcription	Colonic Mucosa	Colon
4	chr1:161285000-161298400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:161285000-161301800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:161285200-161295400	Weak transcription	Primary B cells from cord blood	blood
7	chr1:161285200-161295400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:161285200-161295400	Weak transcription	Fetal Kidney	kidney
9	chr1:161285200-161295400	Weak transcription	Right Ventricle	heart
10	chr1:161285200-161299200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:161285200-161321400	Weak transcription	Stomach Mucosa	stomach
12	chr1:161285400-161295400	Weak transcription	Primary T cells from cord blood	blood
13	chr1:161285400-161295400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:161285400-161295400	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:161285400-161295400	Weak transcription	A549	lung
16	chr1:161285400-161295800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:161285400-161296800	Weak transcription	HSMMtube	muscle
18	chr1:161285400-161298200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:161285400-161298400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:161285400-161299800	Weak transcription	Psoas Muscle	Psoas
21	chr1:161285400-161302000	Weak transcription	Fetal Brain Male	brain
22	chr1:161285400-161303400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:161285400-161303600	Weak transcription	NHLF	lung
24	chr1:161285400-161310200	Weak transcription	HUVEC	blood vessel
25	chr1:161285400-161321400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:161285600-161298200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:161285600-161298200	Weak transcription	HMEC	breast
28	chr1:161285600-161298200	Weak transcription	HSMM	muscle
29	chr1:161285600-161302600	Weak transcription	Esophagus	oesophagus
30	chr1:161285800-161298800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:161286000-161295400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:161286800-161299800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:161286800-161337400	Weak transcription	Fetal Heart	heart
34	chr1:161287000-161337400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:161289600-161317200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:161292600-161299600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:161293200-161295600	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:161293200-161297200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:161293200-161304600	Strong transcription	Fetal Intestine Small	intestine
40	chr1:161293200-161306600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:161293200-161307800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:161293200-161315200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:161293200-161317000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:161293200-161317400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:161293400-161296800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:161293400-161296800	Strong transcription	Fetal Brain Female	brain
47	chr1:161293400-161300000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:161293400-161302000	Strong transcription	Thymus	Thymus
49	chr1:161293400-161307400	Strong transcription	Fetal Stomach	stomach
50	chr1:161293400-161307800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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