Variant report

Variant	rs1994491
Chromosome Location	chr3:45960420-45960421
allele	C/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	NFIC	chr3:45960099-45960678	GM12878	blood:	n/a	n/a
2	EBF1	chr3:45960290-45960569	GM12878	blood:	n/a	n/a
3	RUNX3	chr3:45960146-45960683	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45957988..45959492-chr3:45959750..45961379,2	K562	blood:
2	chr3:45958439..45960531-chr3:46002605..46005170,2	K562	blood:

Variant related genes	Relation type
LZTFL1	TF binding region

Extended variants
information (count: 151 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs13059238	0.91[EUR][1000 genomes]
rs13060287	0.81[EUR][1000 genomes]
rs13063527	1.00[AFR][1000 genomes]
rs13066062	0.94[EUR][1000 genomes]
rs13066516	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13068570	1.00[AFR][1000 genomes]
rs13069079	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13071283	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs13072267	1.00[AFR][1000 genomes]
rs13074382	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs13075528	1.00[AFR][1000 genomes]
rs13075758	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13078739	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs13079869	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs13081151	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13081213	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs13082697	0.81[EUR][1000 genomes]
rs13089554	1.00[AFR][1000 genomes]
rs13089855	0.83[EUR][1000 genomes]
rs13090194	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs13091868	1.00[AFR][1000 genomes]
rs13093179	1.00[AFR][1000 genomes]
rs13095602	1.00[AFR][1000 genomes]
rs13095717	1.00[AFR][1000 genomes]
rs13096741	1.00[AFR][1000 genomes]
rs13097556	0.81[EUR][1000 genomes]
rs13099120	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13433997	0.84[EUR][1000 genomes]
rs1491950	1.00[AFR][1000 genomes]
rs17214952	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs17215008	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17215981	1.00[AFR][1000 genomes]
rs17280623	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs17330872	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17714101	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17714228	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17764831	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17764980	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1994492	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1994493	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2088690	0.81[EUR][1000 genomes]
rs2088692	0.81[EUR][1000 genomes]
rs2102055	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2171531	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2230322	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2373087	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs33910087	0.94[EUR][1000 genomes]
rs34000569	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34047915	1.00[AFR][1000 genomes]
rs34068335	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34093271	1.00[AFR][1000 genomes]
rs34127208	1.00[AFR][1000 genomes]
rs34168660	0.81[EUR][1000 genomes]
rs34283240	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34324101	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34339943	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34340587	1.00[AFR][1000 genomes]
rs34381952	0.96[EUR][1000 genomes]
rs34438204	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34442130	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34452002	1.00[AFR][1000 genomes]
rs34460587	1.00[AFR][1000 genomes]
rs34492478	1.00[AFR][1000 genomes]
rs34493660	0.83[EUR][1000 genomes]
rs34518147	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34562820	0.82[EUR][1000 genomes]
rs34584867	0.81[EUR][1000 genomes]
rs34619093	0.82[EUR][1000 genomes]
rs34679077	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34718164	1.00[AFR][1000 genomes]
rs34754340	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34766614	1.00[AFR][1000 genomes]
rs34774687	0.81[EUR][1000 genomes]
rs34836513	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34849862	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34863575	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34901975	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35110864	1.00[AFR][1000 genomes]
rs35159820	0.81[EUR][1000 genomes]
rs35161099	0.82[EUR][1000 genomes]
rs35209528	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs35280891	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35334665	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35454877	0.81[EUR][1000 genomes]
rs35477280	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs35501575	0.95[EUR][1000 genomes]
rs35516580	1.00[AFR][1000 genomes]
rs35525815	0.95[EUR][1000 genomes]
rs35539222	1.00[AFR][1000 genomes]
rs35669129	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs35751180	0.82[EUR][1000 genomes]
rs35772789	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35814488	0.81[EUR][1000 genomes]
rs35827997	0.96[EUR][1000 genomes]
rs35831747	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35855315	0.95[EUR][1000 genomes]
rs35883205	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35921206	0.81[EUR][1000 genomes]
rs35930050	0.81[EUR][1000 genomes]
rs36023124	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs36039366	0.96[EUR][1000 genomes]
rs36040135	0.81[EUR][1000 genomes]
rs36057789	1.00[AFR][1000 genomes]
rs36122610	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs3851346	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs41289616	0.96[EUR][1000 genomes]
rs41289622	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4362758	0.81[EUR][1000 genomes]
rs4373103	1.00[AFR][1000 genomes]
rs4388012	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs55875328	0.83[EUR][1000 genomes]
rs55920693	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs56332428	0.96[EUR][1000 genomes]
rs60019065	0.81[EUR][1000 genomes]
rs61556067	0.83[EUR][1000 genomes]
rs61650989	0.83[EUR][1000 genomes]
rs67200151	0.83[EUR][1000 genomes]
rs6780028	0.81[EUR][1000 genomes]
rs6782814	0.83[EUR][1000 genomes]
rs6785091	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs6790866	0.81[EUR][1000 genomes]
rs6791016	0.81[EUR][1000 genomes]
rs67937868	0.83[EUR][1000 genomes]
rs71325091	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71325092	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71325095	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs71325096	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs71325098	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs71325100	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs71325101	0.93[EUR][1000 genomes]
rs71325102	0.95[EUR][1000 genomes]
rs71327003	0.85[EUR][1000 genomes]
rs71327006	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs71327007	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs71327009	0.82[EUR][1000 genomes]
rs71327010	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs71327014	1.00[AFR][1000 genomes]
rs71327015	1.00[AFR][1000 genomes]
rs71327017	1.00[AFR][1000 genomes]
rs71327021	1.00[AFR][1000 genomes]
rs71327023	1.00[AFR][1000 genomes]
rs71327024	1.00[AFR][1000 genomes]
rs71327025	1.00[AFR][1000 genomes]
rs71615437	1.00[AFR][1000 genomes]
rs71615438	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7653372	0.89[CEU][hapmap]
rs876668	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45943000-45961000	Weak transcription	Brain Substantia Nigra	brain
2	chr3:45943600-45961200	Weak transcription	Gastric	stomach
3	chr3:45948200-45961000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:45948400-45961600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:45949200-45962400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:45949800-45962600	Weak transcription	HepG2	liver
7	chr3:45950000-45960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
9	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
10	chr3:45953200-45960800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:45956800-45961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:45957400-45960800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:45957400-45961600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:45957400-45963000	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:45957800-45960800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:45957800-45961200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:45957800-45961400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:45957800-45962400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:45957800-45962600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:45957800-45963000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:45957800-45963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:45957800-45963600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:45957800-45963600	Weak transcription	Colonic Mucosa	Colon
27	chr3:45957800-45969000	Weak transcription	K562	blood
28	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:45958000-45960800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:45958000-45960800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:45958000-45960800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:45958000-45960800	Weak transcription	NHLF	lung
33	chr3:45958000-45961000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:45958000-45961400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:45958000-45961400	Weak transcription	HSMMtube	muscle
36	chr3:45958000-45962400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:45958000-45962800	Weak transcription	Brain Germinal Matrix	brain
38	chr3:45958000-45964400	Weak transcription	Stomach Mucosa	stomach
39	chr3:45958000-45964600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:45958000-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:45958000-45965000	Weak transcription	Osteobl	bone
42	chr3:45958000-45965200	Weak transcription	HSMM	muscle
43	chr3:45958000-45969000	Weak transcription	NH-A	brain
44	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:45958200-45961200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:45958200-45961600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:45958200-45963200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:45958200-45963400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:45958400-45963000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:45958400-45966200	Strong transcription	Stomach Smooth Muscle	stomach

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