Variant report

Variant	rs3130377
Chromosome Location	chr6:30323393-30323394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30318532..30322622-chr6:30323241..30327325,5	K562	blood:
2	chr6:30299130..30300961-chr6:30321586..30324149,2	MCF-7	breast:
3	chr6:30323144..30325675-chr6:30329322..30331763,2	K562	blood:
4	chr6:30322834..30325088-chr6:30341151..30343216,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224372	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11158	0.81[EUR][1000 genomes]
rs1573296	0.80[EUR][1000 genomes]
rs1970	0.80[EUR][1000 genomes]
rs2106072	0.81[EUR][1000 genomes]
rs2157678	0.80[EUR][1000 genomes]
rs2517609	0.88[EUR][1000 genomes]
rs2517617	0.88[EUR][1000 genomes]
rs2517622	0.81[EUR][1000 genomes]
rs2523712	0.88[EUR][1000 genomes]
rs2523729	0.81[EUR][1000 genomes]
rs2844777	0.91[EUR][1000 genomes]
rs3094034	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3094036	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3094054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094064	0.98[EUR][1000 genomes]
rs3094066	0.95[EUR][1000 genomes]
rs3094067	0.98[EUR][1000 genomes]
rs3094069	0.95[EUR][1000 genomes]
rs3094078	0.95[EUR][1000 genomes]
rs3094620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094621	0.89[EUR][1000 genomes]
rs3094622	0.89[EUR][1000 genomes]
rs3094624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094628	0.90[EUR][1000 genomes]
rs3129815	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3129830	0.95[EUR][1000 genomes]
rs3130350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130355	0.98[EUR][1000 genomes]
rs3130363	0.86[EUR][1000 genomes]
rs3130364	1.00[EUR][1000 genomes]
rs3130380	0.95[EUR][1000 genomes]
rs3130399	0.95[EUR][1000 genomes]
rs3132647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3130377	ZNF192	cis	cerebellum	SCAN
rs3130377	ZNF323	cis	parietal	SCAN
rs3130377	BTN2A1	cis	parietal	SCAN
rs3130377	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3130377	ZNF192	cis	parietal	SCAN
rs3130377	HIST1H2BM	cis	cerebellum	SCAN
rs3130377	HLA-A	cis	lymphoblastoid	GTEx
rs3130377	ZKSCAN3	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30313800-30325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:30314000-30324200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:30314000-30325600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:30314200-30323400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:30314200-30325600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:30314200-30325600	Weak transcription	Psoas Muscle	Psoas
7	chr6:30314400-30325000	Weak transcription	Esophagus	oesophagus
8	chr6:30314400-30325400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:30314600-30325600	Weak transcription	Pancreas	Pancrea
10	chr6:30315000-30323400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:30315000-30325600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:30315000-30325600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:30315000-30325600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:30315000-30325600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:30315600-30324400	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:30315600-30325400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:30315600-30325400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:30315800-30324200	Weak transcription	Fetal Intestine Large	intestine
19	chr6:30316000-30325600	Weak transcription	Brain Angular Gyrus	brain
20	chr6:30316200-30324400	Weak transcription	Fetal Intestine Small	intestine
21	chr6:30316200-30325800	Weak transcription	Gastric	stomach
22	chr6:30316600-30324200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:30323200-30323400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:30323200-30323400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:30323200-30323400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr6:30323200-30323600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:30323200-30323600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:30323200-30323600	ZNF genes & repeats	Aorta	Aorta

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