Variant report

Variant	rs10169512
Chromosome Location	chr2:30688682-30688683
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30452818..30454421-chr2:30687751..30690665,2	K562	blood:
2	chr2:30668681..30671987-chr2:30686628..30689382,3	K562	blood:

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10169001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170012	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10174170	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10176138	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178307	0.83[EUR][1000 genomes]
rs10178829	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180054	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181161	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10186917	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10197915	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10198587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200589	0.82[EUR][1000 genomes]
rs10200895	0.83[EUR][1000 genomes]
rs10201020	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10204301	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10206659	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10206668	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208587	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210365	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10211659	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10469986	0.83[EUR][1000 genomes]
rs10469987	0.83[EUR][1000 genomes]
rs10514772	0.83[EUR][1000 genomes]
rs1074066	0.83[EUR][1000 genomes]
rs11127277	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11127279	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11885407	0.86[EUR][1000 genomes]
rs11886181	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11896768	0.83[EUR][1000 genomes]
rs11899182	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11901989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903573	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12463548	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465894	0.84[EUR][1000 genomes]
rs12466071	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12466818	0.82[EUR][1000 genomes]
rs12467017	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467646	0.83[EUR][1000 genomes]
rs12467830	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467831	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12468971	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12469630	0.83[EUR][1000 genomes]
rs12469745	0.83[EUR][1000 genomes]
rs12469849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471248	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471868	0.82[EUR][1000 genomes]
rs12474202	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12475104	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12476387	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12476392	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12476805	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12477267	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12478778	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13382540	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13383939	0.83[EUR][1000 genomes]
rs13388031	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13388156	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13388701	0.82[EUR][1000 genomes]
rs13389142	0.83[EUR][1000 genomes]
rs13390344	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13391492	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13393150	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13398796	0.83[EUR][1000 genomes]
rs13401246	0.87[EUR][1000 genomes]
rs13404307	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405340	0.82[EUR][1000 genomes]
rs13408621	0.82[EUR][1000 genomes]
rs13412012	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13413678	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413980	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13414468	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13417949	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13419209	0.82[EUR][1000 genomes]
rs13419435	0.82[EUR][1000 genomes]
rs13422024	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13424441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13427862	0.83[EUR][1000 genomes]
rs13428342	0.83[EUR][1000 genomes]
rs13430515	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430781	0.83[EUR][1000 genomes]
rs13432085	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1404607	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17009601	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17009805	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17009808	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1869425	0.83[EUR][1000 genomes]
rs1869426	0.83[EUR][1000 genomes]
rs1880539	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1880541	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1982286	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1997036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028668	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2077985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2084301	0.83[EUR][1000 genomes]
rs2100112	0.82[EUR][1000 genomes]
rs2100113	0.83[EUR][1000 genomes]
rs2123757	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2166669	0.82[EUR][1000 genomes]
rs2167970	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2363291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363294	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363311	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2363851	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28378040	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816593	0.82[EUR][1000 genomes]
rs4144806	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4951991	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951993	0.83[EUR][1000 genomes]
rs4951994	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951995	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951996	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951997	0.83[EUR][1000 genomes]
rs4951998	0.83[EUR][1000 genomes]
rs4952000	0.82[EUR][1000 genomes]
rs4952003	0.83[EUR][1000 genomes]
rs4952004	0.83[EUR][1000 genomes]
rs4952126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952127	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952129	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952130	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952131	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952133	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4952135	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952136	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952137	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952139	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952141	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952142	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952143	0.81[ASN][1000 genomes]
rs4952145	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952146	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952149	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952150	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4952151	0.82[AFR][1000 genomes]
rs4952152	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952154	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952155	0.86[EUR][1000 genomes]
rs4952158	0.83[EUR][1000 genomes]
rs4952159	0.82[EUR][1000 genomes]
rs4952161	0.83[EUR][1000 genomes]
rs4952162	0.83[EUR][1000 genomes]
rs4952163	0.83[EUR][1000 genomes]
rs4952164	0.83[EUR][1000 genomes]
rs55789733	0.86[EUR][1000 genomes]
rs6723023	0.82[EUR][1000 genomes]
rs6739248	0.83[EUR][1000 genomes]
rs7355326	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7355456	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597579	0.83[EUR][1000 genomes]
rs7603834	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603947	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605131	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs766880	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9309681	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10169512	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671600-30694600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:30678400-30704200	Weak transcription	Fetal Stomach	stomach
5	chr2:30678600-30703800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:30678600-30710600	Weak transcription	NHLF	lung
7	chr2:30682400-30693400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:30682400-30704400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:30683200-30692400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:30685200-30689600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:30687400-30689000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr2:30687400-30689000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr2:30687600-30689600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:30687800-30688800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr2:30688000-30689600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:30688200-30688800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr2:30688200-30697600	Weak transcription	Thymus	Thymus
18	chr2:30688200-30703400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:30688400-30691200	Weak transcription	A549	lung
20	chr2:30688400-30692400	Weak transcription	Ovary	ovary
21	chr2:30688400-30693400	Weak transcription	Fetal Kidney	kidney
22	chr2:30688400-30697200	Weak transcription	Right Ventricle	heart
23	chr2:30688400-30703400	Weak transcription	K562	blood
24	chr2:30688400-30703800	Weak transcription	Left Ventricle	heart
25	chr2:30688400-30704200	Weak transcription	Aorta	Aorta
26	chr2:30688400-30704600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:30688600-30688800	Enhancers	NHDF-Ad	bronchial
28	chr2:30688600-30692800	Weak transcription	HepG2	liver
29	chr2:30688600-30694400	Weak transcription	Fetal Heart	heart
30	chr2:30688600-30695000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:30688600-30695200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:30688600-30710000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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